Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008122.1 Hibiscus syriacus cultivar Beakdansim tig00110676_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: 2511854
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 8
Found at i:1304709 original size:13 final size:13
Alignment explanation
Indices: 1304691--1304715 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1304681 TATTTTAAAT
1304691 ATTTCTTATTATG
1 ATTTCTTATTATG
1304704 ATTTCTTATTAT
1 ATTTCTTATTAT
1304716 TATTCGTAAA
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:0.24, C:0.08, G:0.04, T:0.64
Consensus pattern (13 bp):
ATTTCTTATTATG
Found at i:1305544 original size:14 final size:14
Alignment explanation
Indices: 1305525--1305551 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1305515 GCTTGAAGAA
1305525 AAATAGGAAGACTG
1 AAATAGGAAGACTG
1305539 AAATAGGAAGACT
1 AAATAGGAAGACT
1305552 ACAAAGCTTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.07, G:0.26, T:0.15
Consensus pattern (14 bp):
AAATAGGAAGACTG
Found at i:1307014 original size:21 final size:21
Alignment explanation
Indices: 1306990--1307063 Score: 96
Period size: 21 Copynumber: 3.4 Consensus size: 21
1306980 AAAAAAATTA
1306990 TGTCTTTGTGACATGTTTCTC
1 TGTCTTTGTGACATGTTTCTC
*
1307011 TGTCTTTGTGACATGTTTTTC
1 TGTCTTTGTGACATGTTTCTC
*
1307032 AGTCTTTGTGACACAT-TTATCTC
1 TGTCTTTGTG--ACATGTT-TCTC
1307055 TGTCTTTGT
1 TGTCTTTGT
1307064 TGTATTTTTT
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
21 29 0.63
22 2 0.04
23 15 0.33
ACGTcount: A:0.12, C:0.18, G:0.18, T:0.53
Consensus pattern (21 bp):
TGTCTTTGTGACATGTTTCTC
Found at i:1307358 original size:21 final size:21
Alignment explanation
Indices: 1307329--1307382 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
1307319 GACTAGTTTA
*
1307329 GTGACATGTTTATCTGTCTTT
1 GTGACATGTTTATCTGCCTTT
* *
1307350 GTGATATGTTTCTCTGCCTTT
1 GTGACATGTTTATCTGCCTTT
*
1307371 GTGACATATTTA
1 GTGACATGTTTA
1307383 CCTCCGACTT
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:0.17, C:0.15, G:0.19, T:0.50
Consensus pattern (21 bp):
GTGACATGTTTATCTGCCTTT
Found at i:1312938 original size:29 final size:29
Alignment explanation
Indices: 1312855--1312955 Score: 105
Period size: 29 Copynumber: 3.4 Consensus size: 29
1312845 TTCATTTAAG
* * * *
1312855 TACCTACAGTATTTTGTA-TCAAGATAAA
1 TACCTAAAATATTTTTTAGTCAAAATAAA
* *
1312883 TTCCTAAAATTATCTTTTTGGTCAAAATAAA
1 TACCTAAAA-TAT-TTTTTAGTCAAAATAAA
*
1312914 TACTTAAAATATTTTTTAGTCAAAATAAA
1 TACCTAAAATATTTTTTAGTCAAAATAAA
*
1312943 TACCTAAAGTATT
1 TACCTAAAATATT
1312956 CAATTTTTTC
Statistics
Matches: 59, Mismatches: 11, Indels: 5
0.79 0.15 0.07
Matches are distributed among these distances:
28 6 0.10
29 30 0.51
30 7 0.12
31 16 0.27
ACGTcount: A:0.42, C:0.12, G:0.07, T:0.40
Consensus pattern (29 bp):
TACCTAAAATATTTTTTAGTCAAAATAAA
Found at i:1313111 original size:32 final size:31
Alignment explanation
Indices: 1313065--1313134 Score: 79
Period size: 32 Copynumber: 2.3 Consensus size: 31
1313055 TTTTGACATG
* **
1313065 AAATACTTTATGTATCTCTTTTGATTAAAAA
1 AAATACTTCATGTATCTCTTTTGACCAAAAA
* *
1313096 AAATAACTTCATGTATTTGTTTTGACC-AAAA
1 AAAT-ACTTCATGTATCTCTTTTGACCAAAAA
1313127 AAATACTT
1 AAATACTT
1313135 TAAGTACTTA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
30 4 0.12
31 12 0.36
32 17 0.52
ACGTcount: A:0.40, C:0.11, G:0.07, T:0.41
Consensus pattern (31 bp):
AAATACTTCATGTATCTCTTTTGACCAAAAA
Found at i:1316277 original size:29 final size:29
Alignment explanation
Indices: 1316235--1316316 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
1316225 AAACTAAATT
*
1316235 GATGTCATTGCTTACATCATTTAAGTAAA
1 GATGTCATTGCTTACATCATTTAAATAAA
*
1316264 GATGTCATTGCTTACATCATTTAAATAAT
1 GATGTCATTGCTTACATCATTTAAATAAA
1316293 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
1316317 GTTAGGTAAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.40
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAAATAAA
Found at i:1317604 original size:15 final size:15
Alignment explanation
Indices: 1317581--1317610 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1317571 AGTCGGCTGG
1317581 AATTACAACAATAAC
1 AATTACAACAATAAC
*
1317596 AATTCCAACAATAAC
1 AATTACAACAATAAC
1317611 TATGAGAAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.23, G:0.00, T:0.20
Consensus pattern (15 bp):
AATTACAACAATAAC
Found at i:1321016 original size:29 final size:29
Alignment explanation
Indices: 1320974--1321084 Score: 186
Period size: 29 Copynumber: 3.8 Consensus size: 29
1320964 AAACTAAATT
1320974 GATGTCATTGCTTACATCATTTAAGTAAA
1 GATGTCATTGCTTACATCATTTAAGTAAA
1321003 GATGTCATTGCTTACATCATTTAAGTAAA
1 GATGTCATTGCTTACATCATTTAAGTAAA
* *
1321032 GATGTCATTGCTTACATCATTTAAATAAT
1 GATGTCATTGCTTACATCATTTAAGTAAA
*
1321061 GATGTCATTACTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
1321085 GTTAGGTGAT
Statistics
Matches: 78, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
29 73 0.94
30 5 0.06
ACGTcount: A:0.34, C:0.14, G:0.12, T:0.40
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAAGTAAA
Found at i:1322187 original size:4 final size:4
Alignment explanation
Indices: 1322178--1322203 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
1322168 AAAAATTCTT
1322178 CATA CATA CATA CATA CATA CATA CA
1 CATA CATA CATA CATA CATA CATA CA
1322204 AGACAGATGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.50, C:0.27, G:0.00, T:0.23
Consensus pattern (4 bp):
CATA
Found at i:1325731 original size:16 final size:16
Alignment explanation
Indices: 1325710--1325762 Score: 70
Period size: 16 Copynumber: 3.1 Consensus size: 16
1325700 TAGCTGACCC
1325710 TTATTCCCATATGTAA
1 TTATTCCCATATGTAA
1325726 TTATTCCCATATGTAA
1 TTATTCCCATATGTAA
1325742 TGGGGTATTCCCATATGTAA
1 T----TATTCCCATATGTAA
1325762 T
1 T
1325763 GGGGAAAGGG
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
16 17 0.52
20 16 0.48
ACGTcount: A:0.28, C:0.17, G:0.13, T:0.42
Consensus pattern (16 bp):
TTATTCCCATATGTAA
Found at i:1325752 original size:20 final size:20
Alignment explanation
Indices: 1325711--1325766 Score: 84
Period size: 20 Copynumber: 3.0 Consensus size: 20
1325701 AGCTGACCCT
1325711 TATTCCCATATGTAAT----
1 TATTCCCATATGTAATGGGG
1325727 TATTCCCATATGTAATGGGG
1 TATTCCCATATGTAATGGGG
1325747 TATTCCCATATGTAATGGGG
1 TATTCCCATATGTAATGGGG
1325767 AAAGGGGGAG
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
16 16 0.44
20 20 0.56
ACGTcount: A:0.27, C:0.16, G:0.20, T:0.38
Consensus pattern (20 bp):
TATTCCCATATGTAATGGGG
Found at i:1327851 original size:2 final size:2
Alignment explanation
Indices: 1327844--1327876 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1327834 TGCATTCTTC
1327844 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1327877 GAAATGATGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1330273 original size:15 final size:15
Alignment explanation
Indices: 1330250--1330280 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1330240 TTATTTTATC
1330250 TAAAAATTAAAATGT
1 TAAAAATTAAAATGT
*
1330265 TAAAGATTAAAATGT
1 TAAAAATTAAAATGT
1330280 T
1 T
1330281 TTAATAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.55, C:0.00, G:0.10, T:0.35
Consensus pattern (15 bp):
TAAAAATTAAAATGT
Found at i:1330841 original size:19 final size:21
Alignment explanation
Indices: 1330803--1330841 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
1330793 TATATTTCTA
1330803 AAAAATAAATTATTTATTAAT
1 AAAAATAAATTATTTATTAAT
*
1330824 AAAAA-AAA-TATTTTTTAA
1 AAAAATAAATTATTTATTAA
1330842 AGTTAACTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
20 3 0.18
21 5 0.29
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
AAAAATAAATTATTTATTAAT
Found at i:1335992 original size:18 final size:18
Alignment explanation
Indices: 1335969--1336010 Score: 84
Period size: 18 Copynumber: 2.3 Consensus size: 18
1335959 TTGCGATTCT
1335969 GGACAGACTTAGTACTCA
1 GGACAGACTTAGTACTCA
1335987 GGACAGACTTAGTACTCA
1 GGACAGACTTAGTACTCA
1336005 GGACAG
1 GGACAG
1336011 GTTGTTGAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.33, C:0.21, G:0.26, T:0.19
Consensus pattern (18 bp):
GGACAGACTTAGTACTCA
Found at i:1336603 original size:21 final size:21
Alignment explanation
Indices: 1336577--1336625 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
1336567 AAGGGTCATA
1336577 CAATGAAAGATTAAATCTAAC
1 CAATGAAAGATTAAATCTAAC
*
1336598 CAATGAAATATTAAATCTAAC
1 CAATGAAAGATTAAATCTAAC
1336619 CAA-GAAA
1 CAATGAAA
1336626 CTCAAACAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
20 4 0.15
21 23 0.85
ACGTcount: A:0.55, C:0.14, G:0.08, T:0.22
Consensus pattern (21 bp):
CAATGAAAGATTAAATCTAAC
Found at i:1338311 original size:15 final size:15
Alignment explanation
Indices: 1338266--1338324 Score: 57
Period size: 15 Copynumber: 3.8 Consensus size: 15
1338256 TTTATAATGT
* *
1338266 TAAAATATATTATTT
1 TAAAATATATTAATA
*
1338281 TAATAATATAAATAAT-
1 TAA-AATAT-ATTAATA
1338297 TATAAATATATTAATA
1 TA-AAATATATTAATA
1338313 TAAAATATATTA
1 TAAAATATATTA
1338325 TTTTAATTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
15 18 0.49
16 14 0.38
17 5 0.14
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
TAAAATATATTAATA
Found at i:1338333 original size:24 final size:24
Alignment explanation
Indices: 1338266--1338344 Score: 83
Period size: 24 Copynumber: 3.3 Consensus size: 24
1338256 TTTATAATGT
1338266 TAAAATATATTATTTTAA-TAATA
1 TAAAATATATTATTTTAATTAATA
**
1338289 T-AAATA-ATTATAAATATATTAATA
1 TAAAATATATTAT-TTTA-ATTAATA
* *
1338313 TAAAATATATTATTTTAATTATTT
1 TAAAATATATTATTTTAATTAATA
1338337 TAAAATAT
1 TAAAATAT
1338345 TGATATAATC
Statistics
Matches: 45, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
21 5 0.11
22 7 0.16
23 2 0.04
24 19 0.42
25 7 0.16
26 5 0.11
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (24 bp):
TAAAATATATTATTTTAATTAATA
Found at i:1338641 original size:29 final size:29
Alignment explanation
Indices: 1338595--1338653 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
1338585 GCATTTCGAT
*
1338595 AGTCATTATATAATTAAATTCAGAATTTA
1 AGTCATTATATAAATAAATTCAGAATTTA
*
1338624 AGTCATTATATAAATAAATTCAGATTTTA
1 AGTCATTATATAAATAAATTCAGAATTTA
1338653 A
1 A
1338654 TAGAACTATG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.46, C:0.07, G:0.07, T:0.41
Consensus pattern (29 bp):
AGTCATTATATAAATAAATTCAGAATTTA
Found at i:1343854 original size:142 final size:142
Alignment explanation
Indices: 1343696--1343976 Score: 535
Period size: 142 Copynumber: 2.0 Consensus size: 142
1343686 AGTTGAAAGT
1343696 AAAAAATCTTTTGGCCGATGAAAAGGTGTTTTCGTTCGAGATCGTTTGTATAGATCTACGAAAAC
1 AAAAAATCTTTTGGCCGATGAAAAGGTGTTTTCGTTCGAGATCGTTTGTATAGATCTACGAAAAC
*
1343761 CCGAGGCCTTTTTTTTGAAAAAACAACTTGATTTTCAAAACGAGGAGAAGAAAAGCATTCGGAAA
66 CCGAGGCCTTTTTTTTGAAAAAACAACTTGATTTTCAAAACGAGGAGAAGAAAAGCATTCAGAAA
1343826 AGCAAAAAAAAA
131 AGCAAAAAAAAA
1343838 AAAAAATCTTTTGGCCGATGAAAAGGTGTTTTCGTTCGAGATCGTTTGTATAGATCTACGAAAAC
1 AAAAAATCTTTTGGCCGATGAAAAGGTGTTTTCGTTCGAGATCGTTTGTATAGATCTACGAAAAC
*
1343903 CCGAGGCCTTTTTTTTGAAAAACCAACTTGATTTTCAAAACGAGGAGAAGAAAAGCATTCAGAAA
66 CCGAGGCCTTTTTTTTGAAAAAACAACTTGATTTTCAAAACGAGGAGAAGAAAAGCATTCAGAAA
*
1343968 AGTAAAAAA
131 AGCAAAAAA
1343977 TCTTTTGATT
Statistics
Matches: 136, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
142 136 1.00
ACGTcount: A:0.40, C:0.14, G:0.20, T:0.27
Consensus pattern (142 bp):
AAAAAATCTTTTGGCCGATGAAAAGGTGTTTTCGTTCGAGATCGTTTGTATAGATCTACGAAAAC
CCGAGGCCTTTTTTTTGAAAAAACAACTTGATTTTCAAAACGAGGAGAAGAAAAGCATTCAGAAA
AGCAAAAAAAAA
Found at i:1344394 original size:16 final size:16
Alignment explanation
Indices: 1344375--1344405 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1344365 CCCTACTATT
1344375 ATTATACTATATTTTC
1 ATTATACTATATTTTC
*
1344391 ATTATATTATATTTT
1 ATTATACTATATTTT
1344406 ACTCCCTTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.61
Consensus pattern (16 bp):
ATTATACTATATTTTC
Found at i:1356206 original size:103 final size:105
Alignment explanation
Indices: 1356025--1356452 Score: 656
Period size: 103 Copynumber: 4.1 Consensus size: 105
1356015 GATATTGGAC
* * *
1356025 TCACGACGAAGGGACCGCTGGTTGTCACCAAACATTTCTCCAATTCAGAGCCAATTTCAACTTCA
1 TCACGACGAAGGGACCGCTGGTTGTCAACAAACATCTCTCAAATTCAGAGCCAATTTCAACTTCA
1356090 CAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACT
66 CAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACT
1356130 TCACGACGAAGGGACCGCTGGTTGTCAAC-AACAT-TCTCAAATTCAGAGCCAATTTCAACTTCA
1 TCACGACGAAGGGACCGCTGGTTGTCAACAAACATCTCTCAAATTCAGAGCCAATTTCAACTTCA
*
1356193 CAACGAAGGATATTGGACTCCCGACAACGCAAGTTCAACT
66 CAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACT
* * *
1356233 TCACGACGAAGGGACCGCT-GTTGTCAATAAACATCTCTCAATTTCAGAGCC-ATTTCAACTTCG
1 TCACGACGAAGGGACCGCTGGTTGTCAACAAACATCTCTCAAATTCAGAGCCAATTTCAACTTCA
*
1356296 CAACGAATGATATTGGACTCCA-ACAACGCAAGTTCAACT
66 CAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACT
1356335 TCACGACGAAGGGACCGCTGGTTGTCAACAAACATCTCTC-AATGTCAGAGCCAATTTCAA-TTC
1 TCACGACGAAGGGACCGCTGGTTGTCAACAAACATCTCTCAAAT-TCAGAGCCAATTTCAACTTC
* * * * * *
1356398 ACAGCGAAGGATATTGGACTCAAGA-AGCACAAGCTCGACT
65 ACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACT
*
1356438 TCACAACGAAGGGAC
1 TCACGACGAAGGGAC
1356453 GACTGGCTCA
Statistics
Matches: 298, Mismatches: 19, Indels: 14
0.90 0.06 0.04
Matches are distributed among these distances:
102 46 0.15
103 196 0.66
104 28 0.09
105 28 0.09
ACGTcount: A:0.33, C:0.27, G:0.19, T:0.21
Consensus pattern (105 bp):
TCACGACGAAGGGACCGCTGGTTGTCAACAAACATCTCTCAAATTCAGAGCCAATTTCAACTTCA
CAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACT
Found at i:1356441 original size:205 final size:208
Alignment explanation
Indices: 1356025--1356452 Score: 654
Period size: 205 Copynumber: 2.1 Consensus size: 208
1356015 GATATTGGAC
* *
1356025 TCACGACGAAGGGACCGCTGGTTGTCACCAAACATTTCTCCAATTCAGAGCCAATTTCAACTTCA
1 TCACGACGAAGGGACCGCTGGTTGTCAACAAACATCTCTCCAATTCAGAGCCAATTTCAACTTCA
1356090 CAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGT
66 CAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGT
**
1356155 CAACAACATTCTCAAATTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCCGACAA
131 CAACAACATTCTCAAATTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAA
* *
1356220 CGCAAGTTCAACT
196 CACAAGCTCAACT
*
1356233 TCACGACGAAGGGACCGCT-GTTGTCAATAAACATCTCT-CAATTTCAGAGCC-ATTTCAACTTC
1 TCACGACGAAGGGACCGCTGGTTGTCAACAAACATCTCTCCAA-TTCAGAGCCAATTTCAACTTC
* *
1356295 GCAACGAATGATATTGGACTCCA-ACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTG
65 ACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTG
*
1356359 TCAACAAACATCTCTC-AATGTCAGAGCCAATTTCAA-TTCACAGCGAAGGATATTGGACTCAAG
130 TCAAC-AACAT-TCTCAAAT-TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCAAG
* *
1356422 A-AGCACAAGCTCGACT
192 ACAACACAAGCTCAACT
*
1356438 TCACAACGAAGGGAC
1 TCACGACGAAGGGAC
1356453 GACTGGCTCA
Statistics
Matches: 203, Mismatches: 13, Indels: 11
0.89 0.06 0.05
Matches are distributed among these distances:
205 71 0.35
206 68 0.33
207 45 0.22
208 19 0.09
ACGTcount: A:0.33, C:0.27, G:0.19, T:0.21
Consensus pattern (208 bp):
TCACGACGAAGGGACCGCTGGTTGTCAACAAACATCTCTCCAATTCAGAGCCAATTTCAACTTCA
CAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGT
CAACAACATTCTCAAATTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAA
CACAAGCTCAACT
Found at i:1356479 original size:205 final size:205
Alignment explanation
Indices: 1356025--1356504 Score: 634
Period size: 205 Copynumber: 2.3 Consensus size: 205
1356015 GATATTGGAC
* **
1356025 TCACGACGAAGGGACCGCTGGTTGTCACCAAACATTTCTCCAA-TTCAGAGCCAATTTCAACTTC
1 TCACAACGAAGGGACCGCT-G-TGTCAAGAAACATTTCT-CAATTTCAGAGCC-ATTTCAACTTC
1356089 ACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTG
62 ACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTG
**
1356154 TCAACAACATTCTCAAATTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCCGACA
127 TCAACAACATTCTCAAATTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACA
* *
1356219 ACGCAAGTTCAACT
192 ACACAAGCTCAACT
* * * *
1356233 TCACGACGAAGGGACCGCTGTTGTCAATAAACATCTCTCAATTTCAGAGCCATTTCAACTTCGCA
1 TCACAACGAAGGGACCGCTG-TGTCAAGAAACATTTCTCAATTTCAGAGCCATTTCAACTTCACA
*
1356298 ACGAATGATATTGGACTCCA-ACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCA
65 ACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCA
*
1356362 ACAAACATCTCTC-AATGTCAGAGCCAATTTCAA-TTCACAGCGAAGGATATTGGACTCAAGA-A
130 AC-AACAT-TCTCAAAT-TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACA
* *
1356424 GCACAAGCTCGACT
192 ACACAAGCTCAACT
* *
1356438 TCACAACGAAGGGA-CGACTG-GCTCAACGAATA-ATTTCTCAATTCCATAGCCATTTCCAACTT
1 TCACAACGAAGGGACCG-CTGTG-TCAA-GAA-ACATTTCTCAATTTCAGAGCCATTT-CAACTT
1356500 CACAA
61 CACAA
1356505 ACAGATTGAC
Statistics
Matches: 245, Mismatches: 18, Indels: 20
0.87 0.06 0.07
Matches are distributed among these distances:
203 1 0.00
204 6 0.02
205 95 0.39
206 79 0.32
207 45 0.18
208 19 0.08
ACGTcount: A:0.33, C:0.27, G:0.18, T:0.22
Consensus pattern (205 bp):
TCACAACGAAGGGACCGCTGTGTCAAGAAACATTTCTCAATTTCAGAGCCATTTCAACTTCACAA
CGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAA
CAACATTCTCAAATTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAACAC
AAGCTCAACT
Found at i:1356502 original size:103 final size:103
Alignment explanation
Indices: 1356025--1356504 Score: 611
Period size: 103 Copynumber: 4.6 Consensus size: 103
1356015 GATATTGGAC
*
1356025 TCACGACGAAGGGACCGCTGGTTGTCACCAAACATTTCTCCAATTCAGAGCCAATTTCAACTTCA
1 TCACGACGAAGGGACCGCTGG-TGTCAACAAACATTTCT-CAATTCAGAGCCAATTTCAACTTCA
*
1356090 CAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACT
64 CAACGAAGGATATTGGACTCAAGACAACGCAAGTTCAACT
1356130 TCACGACGAAGGGACCGCTGGTTGTCAAC-AACA-TTCTCAAATTCAGAGCCAATTTCAACTTCA
1 TCACGACGAAGGGACCGCTGG-TGTCAACAAACATTTCTC-AATTCAGAGCCAATTTCAACTTCA
**
1356193 CAACGAAGGATATTGGACTCCCGACAACGCAAGTTCAACT
64 CAACGAAGGATATTGGACTCAAGACAACGCAAGTTCAACT
* * * *
1356233 TCACGACGAAGGGACCGCTGTTGTCAATAAACATCTCTCAATTTCAGAGCC-ATTTCAACTTCGC
1 TCACGACGAAGGGACCGCTGGTGTCAACAAACATTTCTCAA-TTCAGAGCCAATTTCAACTTCAC
* *
1356297 AACGAATGATATTGGACTCCA-ACAACGCAAGTTCAACT
65 AACGAAGGATATTGGACTCAAGACAACGCAAGTTCAACT
*
1356335 TCACGACGAAGGGACCGCTGGTTGTCAACAAACATCTCTCAATGTCAGAGCCAATTTCAA-TTCA
1 TCACGACGAAGGGACCGCTGG-TGTCAACAAACATTTCTCAAT-TCAGAGCCAATTTCAACTTCA
* * * * *
1356399 CAGCGAAGGATATTGGACTCAAGA-AGCACAAGCTCGACT
64 CAACGAAGGATATTGGACTCAAGACAACGCAAGTTCAACT
* * *
1356438 TCACAACGAAGGGA-CGACTGG-CTCAACGAATA-ATTTCTCAATTCCATAGCC-ATTTCCAACT
1 TCACGACGAAGGGACCG-CTGGTGTCAAC-AA-ACATTTCTCAATT-CAGAGCCAATTT-CAACT
1356499 TCACAA
61 TCACAA
1356505 ACAGATTGAC
Statistics
Matches: 338, Mismatches: 23, Indels: 30
0.86 0.06 0.08
Matches are distributed among these distances:
101 10 0.03
102 67 0.20
103 208 0.62
104 25 0.07
105 28 0.08
ACGTcount: A:0.33, C:0.27, G:0.18, T:0.22
Consensus pattern (103 bp):
TCACGACGAAGGGACCGCTGGTGTCAACAAACATTTCTCAATTCAGAGCCAATTTCAACTTCACA
ACGAAGGATATTGGACTCAAGACAACGCAAGTTCAACT
Found at i:1356880 original size:2 final size:2
Alignment explanation
Indices: 1356863--1356932 Score: 101
Period size: 2 Copynumber: 36.5 Consensus size: 2
1356853 TACATTACAT
* *
1356863 TA TA T- TA TA TA CA TA TA TA TA TA TA TA TA T- TA TC TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1356902 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
1356933 TACATATGGT
Statistics
Matches: 61, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
1 3 0.05
2 58 0.95
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1357723 original size:140 final size:138
Alignment explanation
Indices: 1357470--1357746 Score: 475
Period size: 140 Copynumber: 2.0 Consensus size: 138
1357460 AGTTGAAAGT
1357470 AAAAAATCTTTTGGCCGATGAAAAGGTGTTCGTTCGAGATCGTTTGTATAGATCTACGAAACCCG
1 AAAAAATCTTTTGGCCGATGAAAAGGTGTTCGTTCGAGATCGTTTGTATAGATCTACGAAACCCG
*
1357535 AGGCCTTTTTTTTTAAAAAAACAACTTGATTTTCAAAACGAGGAGAAGAAAAGCATTCGGAAAAG
66 AGGCC-TTTTTTTTAAAAAAACAACTTGATTTTCAAAACGAGGAGAAGAAAAGCATTCAGAAAAG
1357600 CAAAAAAAA
130 CAAAAAAAA
1357609 AAAAAATCTTTTGGCCGATGAAAAGGTGTTTTCGTTCGAGATCGTTTGTATAGATCTACGAAAAC
1 AAAAAATCTTTTGGCCGATGAAAAGGTG--TTCGTTCGAGATCGTTTGTATAGATCTACG-AAAC
* *
1357674 CCGAGGCC-TTTTTTTGAAAAACCAACTTGATTTTCAAAACGAGGAGAAGAAAAGCATTCAGAAA
63 CCGAGGCCTTTTTTTTAAAAAAACAACTTGATTTTCAAAACGAGGAGAAGAAAAGCATTCAGAAA
*
1357738 AGTAAAAAA
128 AGCAAAAAA
1357747 TCTTTTGATT
Statistics
Matches: 131, Mismatches: 4, Indels: 5
0.94 0.03 0.04
Matches are distributed among these distances:
139 28 0.21
140 61 0.47
141 30 0.23
142 12 0.09
ACGTcount: A:0.40, C:0.14, G:0.19, T:0.26
Consensus pattern (138 bp):
AAAAAATCTTTTGGCCGATGAAAAGGTGTTCGTTCGAGATCGTTTGTATAGATCTACGAAACCCG
AGGCCTTTTTTTTAAAAAAACAACTTGATTTTCAAAACGAGGAGAAGAAAAGCATTCAGAAAAGC
AAAAAAAA
Found at i:1358386 original size:10 final size:10
Alignment explanation
Indices: 1358344--1358402 Score: 55
Period size: 10 Copynumber: 5.3 Consensus size: 10
1358334 TTTACTCCCT
1358344 TATTTTATATA
1 TATTTTAT-TA
1358355 TATATCTTATGTA
1 TAT-T-TTAT-TA
*
1358368 TATTTTTATTT
1 TA-TTTTATTA
1358379 TATTTTATTA
1 TATTTTATTA
1358389 TATTTTATATA
1 TATTTTAT-TA
1358400 TAT
1 TAT
1358403 ATATACCCAT
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
10 15 0.37
11 11 0.27
12 5 0.12
13 9 0.22
14 1 0.02
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.66
Consensus pattern (10 bp):
TATTTTATTA
Found at i:1358401 original size:11 final size:11
Alignment explanation
Indices: 1358344--1358402 Score: 59
Period size: 11 Copynumber: 5.3 Consensus size: 11
1358334 TTTACTCCCT
1358344 TATTTTATATA
1 TATTTTATATA
*
1358355 TATATCTTATGTA
1 TAT-T-TTATATA
*
1358368 TATTTT-TATTT
1 TATTTTATA-TA
1358379 TATTTTAT-TA
1 TATTTTATATA
1358389 TATTTTATATA
1 TATTTTATATA
1358400 TAT
1 TAT
1358403 ATATACCCAT
Statistics
Matches: 39, Mismatches: 4, Indels: 10
0.74 0.08 0.19
Matches are distributed among these distances:
10 10 0.26
11 17 0.44
12 3 0.08
13 9 0.23
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.66
Consensus pattern (11 bp):
TATTTTATATA
Found at i:1361044 original size:53 final size:51
Alignment explanation
Indices: 1360965--1361071 Score: 196
Period size: 53 Copynumber: 2.1 Consensus size: 51
1360955 TCATATTGGA
1360965 TTAAAGCAATGCCAAATAACACTAGAGATAAGGACTATTTTCCTCCACAAG
1 TTAAAGCAATGCCAAATAACACTAGAGATAAGGACTATTTTCCTCCACAAG
1361016 TTAAAGCAATGTCCAAATTAACACTAGAGATAAGGACTATTTTCCTCCACAAG
1 TTAAAGCAATG-CCAAA-TAACACTAGAGATAAGGACTATTTTCCTCCACAAG
1361069 TTA
1 TTA
1361072 CAGAAGTGGT
Statistics
Matches: 54, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
51 11 0.20
52 5 0.09
53 38 0.70
ACGTcount: A:0.40, C:0.21, G:0.13, T:0.26
Consensus pattern (51 bp):
TTAAAGCAATGCCAAATAACACTAGAGATAAGGACTATTTTCCTCCACAAG
Found at i:1362803 original size:17 final size:18
Alignment explanation
Indices: 1362756--1362805 Score: 57
Period size: 19 Copynumber: 2.8 Consensus size: 18
1362746 TTAGATTTAC
* *
1362756 TATTATACTTCTAAATAT
1 TATTATAATTTTAAATAT
1362774 TCATTATAATTTTAAATAT
1 T-ATTATAATTTTAAATAT
*
1362793 T-TTATATTTTTAA
1 TATTATAATTTTAA
1362806 TAAAATCAAC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
17 11 0.39
18 1 0.04
19 16 0.57
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (18 bp):
TATTATAATTTTAAATAT
Found at i:1364351 original size:2 final size:2
Alignment explanation
Indices: 1364346--1364400 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
1364336 AATTCAGCAA
1364346 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
1364388 AT AT AT AT AT AT A
1 AT AT AT AT AT AT A
1364401 GAAGTTGGAT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1373053 original size:78 final size:78
Alignment explanation
Indices: 1372984--1373827 Score: 1222
Period size: 78 Copynumber: 10.8 Consensus size: 78
1372974 CTCCAAGAGG
* ** *
1372984 TAGTATTTTCACGACGAACTCATTAGAGATAGGAGGACTGCGAGGGTCGTTGTGAAGAGGATCTG
1 TAGTCTTTTCACGACGAACTCATTAGAGGCAGGAGGGCTGCGAGGGTCGTTGTGAAGAGGATCTG
1373049 GTCCTCCAGGTGT
66 GTCCTCCAGGTGT
*
1373062 TAGTCTTTTCACGACGAAATCATTAGAGGCAGGAGGGCTGCGAGGGTCGTTGTGAAGAGGATCTG
1 TAGTCTTTTCACGACGAACTCATTAGAGGCAGGAGGGCTGCGAGGGTCGTTGTGAAGAGGATCTG
1373127 GTCCTCCAGGTGT
66 GTCCTCCAGGTGT
* *
1373140 TAGTCTTTTCACGACGAACTCATTAGAGGCAGGAGGGTTGCGAGGGTCTTTGTGAAGAGGATCTG
1 TAGTCTTTTCACGACGAACTCATTAGAGGCAGGAGGGCTGCGAGGGTCGTTGTGAAGAGGATCTG
*
1373205 GACCTCCAGGTGT
66 GTCCTCCAGGTGT
* * * *
1373218 TAGTCTCTTCATGTCGAACTCATTAGAGGCAGGAGGACTGCGAGGGTCGTTGTGAAGAGGATCTG
1 TAGTCTTTTCACGACGAACTCATTAGAGGCAGGAGGGCTGCGAGGGTCGTTGTGAAGAGGATCTG
1373283 GTCCTCCAGGTGT
66 GTCCTCCAGGTGT
1373296 TAGTCTTTTCACGACGAACTCATTAGAGGCAGGAGGGCTGCGAGGGTCGTTGTGAAGAGGATCTG
1 TAGTCTTTTCACGACGAACTCATTAGAGGCAGGAGGGCTGCGAGGGTCGTTGTGAAGAGGATCTG
1373361 GTCCTCCAGGTGT
66 GTCCTCCAGGTGT
1373374 TAGTCTTTTCACGACGAACTCATTAGAGGCAGGAGGGCTGCGAGGGTCGTTGTGAAGAGGATCTG
1 TAGTCTTTTCACGACGAACTCATTAGAGGCAGGAGGGCTGCGAGGGTCGTTGTGAAGAGGATCTG
*
1373439 GACCTCCAGGTGT
66 GTCCTCCAGGTGT
* * *
1373452 TAGTCTTTTCACGACGAACTCATTAGAGGCAGGAGGGTTGCGAGGGTCGTTGTGCAGAGGATATG
1 TAGTCTTTTCACGACGAACTCATTAGAGGCAGGAGGGCTGCGAGGGTCGTTGTGAAGAGGATCTG
1373517 GTCCTCCAGGTGT
66 GTCCTCCAGGTGT
** * * * *
1373530 TAACCTCTTCACGACGAACTCATTAGAGGCAGGAGGGCTGCGAGGATCATTGTGAAGAGGATATG
1 TAGTCTTTTCACGACGAACTCATTAGAGGCAGGAGGGCTGCGAGGGTCGTTGTGAAGAGGATCTG
*
1373595 GACCTCCAGGTGT
66 GTCCTCCAGGTGT
* * * * ** *
1373608 TAGTTTTTTCACGACGAACTCATTAGAGGCAGGAGGACTGAGAGGTTTATTG-GTAAGAGGATAT
1 TAGTCTTTTCACGACGAACTCATTAGAGGCAGGAGGGCTGCGAGGGTCGTTGTG-AAGAGGATCT
* *
1373672 GGACCTCCAGGGGT
65 GGTCCTCCAGGTGT
* * * * * * *
1373686 TAGTCTCTTCACCACGAACTCATTAGAGGGAAGAGGGTTGCGAGGATCATTGTGAAGAGGATCTG
1 TAGTCTTTTCACGACGAACTCATTAGAGGCAGGAGGGCTGCGAGGGTCGTTGTGAAGAGGATCTG
1373751 GTCCTCCAGGTGT
66 GTCCTCCAGGTGT
* * * * * * * * ** *
1373764 TGGTCTCTTCACGGCGAACTCATTAGATGTAGGAGGACTGAGAGGTTTATTGTGAAGAAGATCT
1 TAGTCTTTTCACGACGAACTCATTAGAGGCAGGAGGGCTGCGAGGGTCGTTGTGAAGAGGATCT
1373828 AATACACTCG
Statistics
Matches: 697, Mismatches: 67, Indels: 4
0.91 0.09 0.01
Matches are distributed among these distances:
77 1 0.00
78 695 1.00
79 1 0.00
ACGTcount: A:0.23, C:0.18, G:0.33, T:0.26
Consensus pattern (78 bp):
TAGTCTTTTCACGACGAACTCATTAGAGGCAGGAGGGCTGCGAGGGTCGTTGTGAAGAGGATCTG
GTCCTCCAGGTGT
Found at i:1380488 original size:21 final size:21
Alignment explanation
Indices: 1380462--1380501 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1380452 CAGAACCCCA
*
1380462 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
1380483 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
1380502 TCAAAGGAGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:1380534 original size:21 final size:21
Alignment explanation
Indices: 1380483--1380545 Score: 81
Period size: 21 Copynumber: 2.9 Consensus size: 21
1380473 ATTCCCCTGT
1380483 GGGGGGAATCGGTTCCCCTTCAA
1 GGGGGGAATCGGTT-CCC-TCAA
* *
1380506 AGGAGGAATCGGTTCCCTCAA
1 GGGGGGAATCGGTTCCCTCAA
*
1380527 GGGGGGAATCGATTCCCTC
1 GGGGGGAATCGGTTCCCTC
1380546 TGCACCAAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
21 20 0.57
22 3 0.09
23 12 0.34
ACGTcount: A:0.21, C:0.25, G:0.33, T:0.21
Consensus pattern (21 bp):
GGGGGGAATCGGTTCCCTCAA
Found at i:1387534 original size:27 final size:27
Alignment explanation
Indices: 1387496--1387548 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
1387486 ACAATATGGG
1387496 AATGCAAGTTGGACAAAAAGAAATTCT
1 AATGCAAGTTGGACAAAAAGAAATTCT
*
1387523 AATGCAAGTTGGACATAAAGAAATTC
1 AATGCAAGTTGGACAAAAAGAAATTC
1387549 CACATTTCCT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.47, C:0.11, G:0.19, T:0.23
Consensus pattern (27 bp):
AATGCAAGTTGGACAAAAAGAAATTCT
Found at i:1388632 original size:35 final size:37
Alignment explanation
Indices: 1388588--1388681 Score: 115
Period size: 36 Copynumber: 2.6 Consensus size: 37
1388578 ATTTATGTCT
* *
1388588 TTAAAGTAATGTATTA-GGTTTTTTG-TTTTATCTTC
1 TTAATGTAATGTATTATGGTTTATTGTTTTTATCTTC
*
1388623 TTAATGTAA--TATTCATGGTTCATTGTTTTTATCTTC
1 TTAATGTAATGTATT-ATGGTTTATTGTTTTTATCTTC
*
1388659 TTAATGTAATGTTTTATGGTTTA
1 TTAATGTAATGTATTATGGTTTA
1388682 ATTTAATGTT
Statistics
Matches: 49, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
33 4 0.08
34 1 0.02
35 15 0.31
36 19 0.39
37 7 0.14
38 3 0.06
ACGTcount: A:0.23, C:0.06, G:0.14, T:0.56
Consensus pattern (37 bp):
TTAATGTAATGTATTATGGTTTATTGTTTTTATCTTC
Found at i:1388695 original size:19 final size:20
Alignment explanation
Indices: 1388659--1388699 Score: 66
Period size: 19 Copynumber: 2.1 Consensus size: 20
1388649 TTTTATCTTC
1388659 TTAATGTAATGTTTTATGGT
1 TTAATGTAATGTTTTATGGT
*
1388679 TTAATTTAATG-TTTATGGT
1 TTAATGTAATGTTTTATGGT
1388698 TT
1 TT
1388700 GTTGTTCTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 10 0.50
20 10 0.50
ACGTcount: A:0.24, C:0.00, G:0.17, T:0.59
Consensus pattern (20 bp):
TTAATGTAATGTTTTATGGT
Found at i:1390394 original size:21 final size:20
Alignment explanation
Indices: 1390362--1390401 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
1390352 TCTTTTGTCA
*
1390362 TGATCATTACAGTATTGATG
1 TGATAATTACAGTATTGATG
1390382 TGATAATTCACAGTATTGAT
1 TGATAATT-ACAGTATTGAT
1390402 ATGACGGTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.33, C:0.10, G:0.17, T:0.40
Consensus pattern (20 bp):
TGATAATTACAGTATTGATG
Found at i:1391143 original size:14 final size:14
Alignment explanation
Indices: 1391114--1391159 Score: 65
Period size: 14 Copynumber: 3.1 Consensus size: 14
1391104 CGTTCGTGAA
1391114 CGTTCGATTATATGTT
1 CGTTCG-TT-TATGTT
1391130 CGTTCGTTTATGTT
1 CGTTCGTTTATGTT
*
1391144 CGTTCATTTATGTT
1 CGTTCGTTTATGTT
1391158 CG
1 CG
1391160 AACAGAGGGC
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
14 21 0.72
15 2 0.07
16 6 0.21
ACGTcount: A:0.13, C:0.15, G:0.20, T:0.52
Consensus pattern (14 bp):
CGTTCGTTTATGTT
Found at i:1391329 original size:16 final size:16
Alignment explanation
Indices: 1391308--1391339 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
1391298 TATTCAAACA
1391308 AATTAACTCTAAAGTT
1 AATTAACTCTAAAGTT
1391324 AATTAACTCTAAAGTT
1 AATTAACTCTAAAGTT
1391340 GCAGGTTATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.12, G:0.06, T:0.38
Consensus pattern (16 bp):
AATTAACTCTAAAGTT
Found at i:1391481 original size:14 final size:14
Alignment explanation
Indices: 1391462--1391490 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1391452 GTTTATTATT
1391462 TAAATGAACGAACA
1 TAAATGAACGAACA
1391476 TAAATGAACGAACA
1 TAAATGAACGAACA
1391490 T
1 T
1391491 GAACAAGTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.55, C:0.14, G:0.14, T:0.17
Consensus pattern (14 bp):
TAAATGAACGAACA
Found at i:1394183 original size:66 final size:66
Alignment explanation
Indices: 1394073--1394204 Score: 201
Period size: 66 Copynumber: 2.0 Consensus size: 66
1394063 TAACTATACT
* * * * * *
1394073 CCAAAAATCGAGTTGGACTAAGATTATTGTCTTGAATTTGATAAAATTTAGTAAAAGATAAATTA
1 CCAAAAATCGAGTTCGACTAAAATTATTATCTTAAATGTCATAAAATTTAGTAAAAGATAAATTA
1394138 A
66 A
*
1394139 CCAAAAATCGAGTTCGATTAAAATTATTATCTTAAATGTCATAAAATTTAGTAAAAGATAAATTA
1 CCAAAAATCGAGTTCGACTAAAATTATTATCTTAAATGTCATAAAATTTAGTAAAAGATAAATTA
1394204 A
66 A
1394205 ATTGTTAGTT
Statistics
Matches: 59, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
66 59 1.00
ACGTcount: A:0.46, C:0.08, G:0.12, T:0.33
Consensus pattern (66 bp):
CCAAAAATCGAGTTCGACTAAAATTATTATCTTAAATGTCATAAAATTTAGTAAAAGATAAATTA
A
Found at i:1404983 original size:36 final size:36
Alignment explanation
Indices: 1404941--1405018 Score: 99
Period size: 36 Copynumber: 2.2 Consensus size: 36
1404931 TTTTTATATT
1404941 TATATTATTAAAATA-AT-TTAACTGTTTAAAATA-TAA
1 TATATTATTAAAATATATATT-A-T-TTTAAAATATTAA
*
1404977 TATATTATTATAATATATATTATTTTAAAATATTAA
1 TATATTATTAAAATATATATTATTTTAAAATATTAA
1405013 TATATT
1 TATATT
1405019 TGGTTTAGGT
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
35 9 0.24
36 24 0.63
37 3 0.08
38 2 0.05
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.50
Consensus pattern (36 bp):
TATATTATTAAAATATATATTATTTTAAAATATTAA
Found at i:1405009 original size:15 final size:15
Alignment explanation
Indices: 1404975--1405009 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
1404965 TTTAAAATAT
1404975 AATATATTATTATAA
1 AATATATTATTATAA
* *
1404990 TATATATTATTTTAA
1 AATATATTATTATAA
1405005 AATAT
1 AATAT
1405010 TAATATATTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
AATATATTATTATAA
Found at i:1405019 original size:18 final size:17
Alignment explanation
Indices: 1404965--1405019 Score: 67
Period size: 18 Copynumber: 3.1 Consensus size: 17
1404955 AATTTAACTG
1404965 TTTAAAATATAATATAT
1 TTTAAAATATAATATAT
*
1404982 TATTATAATAT-ATATTAT
1 T-TTAAAATATAATA-TAT
1405000 TTTAAAATATTAATATAT
1 TTTAAAATA-TAATATAT
1405018 TT
1 TT
1405020 GGTTTAGGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
17 11 0.34
18 18 0.56
19 3 0.09
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TTTAAAATATAATATAT
Found at i:1406352 original size:86 final size:86
Alignment explanation
Indices: 1406243--1406409 Score: 298
Period size: 86 Copynumber: 1.9 Consensus size: 86
1406233 ACAAATGCTG
*
1406243 GTTCATACAGTTATAAAGTCCACTTGTATAGTGTAGAAACATCCCAATTGTTTCAAATTTGATGA
1 GTTCATACAGTTATAAAGTCCACTTGTATAGTATAGAAACATCCCAATTGTTTCAAATTTGATGA
1406308 GTACAAATGCTGGTTCGTAGA
66 GTACAAATGCTGGTTCGTAGA
* * *
1406329 GTTCATACAGTTATGAAGTCCACTTGTATAGTATATAAGCATCCCAATTGTTTCAAATTTGATGA
1 GTTCATACAGTTATAAAGTCCACTTGTATAGTATAGAAACATCCCAATTGTTTCAAATTTGATGA
1406394 GTACAAATGCTGGTTC
66 GTACAAATGCTGGTTC
1406410 ACACAGTTCA
Statistics
Matches: 77, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
86 77 1.00
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.35
Consensus pattern (86 bp):
GTTCATACAGTTATAAAGTCCACTTGTATAGTATAGAAACATCCCAATTGTTTCAAATTTGATGA
GTACAAATGCTGGTTCGTAGA
Found at i:1411219 original size:32 final size:32
Alignment explanation
Indices: 1411175--1411235 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 32
1411165 CAACTCTAAT
* **
1411175 TATACAATATACTCTAGTTATGATATTAAAAC
1 TATACAACATACTCTAAATATGATATTAAAAC
*
1411207 TATACAACATACTTTAAATATGATATTAA
1 TATACAACATACTCTAAATATGATATTAA
1411236 GGGTCTGTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.46, C:0.11, G:0.05, T:0.38
Consensus pattern (32 bp):
TATACAACATACTCTAAATATGATATTAAAAC
Found at i:1411283 original size:14 final size:14
Alignment explanation
Indices: 1411264--1411322 Score: 57
Period size: 14 Copynumber: 4.1 Consensus size: 14
1411254 GTAATTGATT
*
1411264 TTCTGGAAATTGAA
1 TTCTGGAAAATGAA
*
1411278 TTCTGGAAAATAAA
1 TTCTGGAAAATGAA
* *
1411292 TTAAT-GAAATTTGAA
1 TT-CTGGAAA-ATGAA
1411307 TTCTGGAAAATGAA
1 TTCTGGAAAATGAA
1411321 TT
1 TT
1411323 ATATTTTTTG
Statistics
Matches: 35, Mismatches: 7, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
14 25 0.71
15 10 0.29
ACGTcount: A:0.42, C:0.05, G:0.17, T:0.36
Consensus pattern (14 bp):
TTCTGGAAAATGAA
Found at i:1411310 original size:29 final size:28
Alignment explanation
Indices: 1411269--1411323 Score: 92
Period size: 29 Copynumber: 1.9 Consensus size: 28
1411259 TGATTTTCTG
1411269 GAAATTGAATTCTGGAAAATAAATTAAT
1 GAAATTGAATTCTGGAAAATAAATTAAT
*
1411297 GAAATTTGAATTCTGGAAAATGAATTA
1 GAAA-TTGAATTCTGGAAAATAAATTA
1411324 TATTTTTTGG
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 4 0.16
29 21 0.84
ACGTcount: A:0.47, C:0.04, G:0.16, T:0.33
Consensus pattern (28 bp):
GAAATTGAATTCTGGAAAATAAATTAAT
Found at i:1411802 original size:34 final size:33
Alignment explanation
Indices: 1411712--1411803 Score: 82
Period size: 34 Copynumber: 2.8 Consensus size: 33
1411702 ATATTATTAG
* * *
1411712 ATTATTA-TATTAATATTAAAT-ATATAAATAAT
1 ATTATTATTATGAATAATAAATAAT-TTAATAAT
* *
1411744 ATTATTAATTATTAATAATTAATAATTTAATAAT
1 ATTATT-ATTATGAATAATAAATAATTTAATAAT
1411778 ATTATT-TCTATGAATTAATAAATAAT
1 ATTATTAT-TATGAA-TAATAAATAAT
1411804 ATAAATTTTA
Statistics
Matches: 50, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
32 7 0.14
33 6 0.12
34 35 0.70
35 2 0.04
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (33 bp):
ATTATTATTATGAATAATAAATAATTTAATAAT
Found at i:1411918 original size:22 final size:24
Alignment explanation
Indices: 1411888--1411955 Score: 70
Period size: 23 Copynumber: 3.0 Consensus size: 24
1411878 ATTATTTTAT
* *
1411888 TATAATATTAAAAATA-TAAT-AC
1 TATATTATTAAAAATATTAATAAA
*
1411910 TATATTATTATAAATATTAATAAA
1 TATATTATTAAAAATATTAATAAA
* *
1411934 TATATT-TTAAATATTTTAATAA
1 TATATTATTAAAAATATTAATAA
1411956 TTAATATTTT
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
22 14 0.37
23 17 0.45
24 7 0.18
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (24 bp):
TATATTATTAAAAATATTAATAAA
Found at i:1423260 original size:24 final size:24
Alignment explanation
Indices: 1423228--1423275 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
1423218 TTAAAATTCG
1423228 ACCCTACTTGATTCGAATAAGTAC
1 ACCCTACTTGATTCGAATAAGTAC
1423252 ACCCTACTTGATTCGAATAAGTAC
1 ACCCTACTTGATTCGAATAAGTAC
1423276 GCATTAAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.33, C:0.25, G:0.12, T:0.29
Consensus pattern (24 bp):
ACCCTACTTGATTCGAATAAGTAC
Found at i:1430898 original size:26 final size:26
Alignment explanation
Indices: 1430852--1430906 Score: 76
Period size: 26 Copynumber: 2.1 Consensus size: 26
1430842 GCCACAGCTA
*
1430852 CTCACCTCCCAGACCGCATCG-CTTAC
1 CTCACCTCCCAGACCGAATCGACTT-C
*
1430878 CTCACCTCCCAGACTGAATCGACTTC
1 CTCACCTCCCAGACCGAATCGACTTC
1430904 CTC
1 CTC
1430907 TCCAATTTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
26 23 0.88
27 3 0.12
ACGTcount: A:0.20, C:0.47, G:0.11, T:0.22
Consensus pattern (26 bp):
CTCACCTCCCAGACCGAATCGACTTC
Found at i:1431546 original size:59 final size:60
Alignment explanation
Indices: 1431463--1431582 Score: 197
Period size: 59 Copynumber: 2.0 Consensus size: 60
1431453 TCTTTTTAAC
* *
1431463 CTAGGATTTGCATATGCCCAATAAGGAAAGTTGGTACACGTATTTACTTGCTGATCAATTT
1 CTAGGATTTGCA-ATGACCAATAAGGAAAGTTGGTACACATATTTACTTGCTGATCAATTT
*
1431524 CTAGGATTTGC-ATGACCAATAAGGAAAGTTGGTCCACATATTTACTTGCTGATCAATTT
1 CTAGGATTTGCAATGACCAATAAGGAAAGTTGGTACACATATTTACTTGCTGATCAATTT
1431583 AATTAATATT
Statistics
Matches: 56, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
59 45 0.80
61 11 0.20
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Consensus pattern (60 bp):
CTAGGATTTGCAATGACCAATAAGGAAAGTTGGTACACATATTTACTTGCTGATCAATTT
Found at i:1436120 original size:36 final size:36
Alignment explanation
Indices: 1436080--1436153 Score: 107
Period size: 36 Copynumber: 2.1 Consensus size: 36
1436070 TGTGATTTTC
*
1436080 TTTTTCAAAAAA-TC-AAAATTTTATATATTTTAAATA
1 TTTTT-AAAAAATTCTAAAATTTTATATA-ATTAAATA
1436116 TTTTTAAAAAATTCTAAAATTTTATATAATTAAATA
1 TTTTTAAAAAATTCTAAAATTTTATATAATTAAATA
1436152 TT
1 TT
1436154 ATTTTTATAT
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
35 6 0.17
36 16 0.46
37 13 0.37
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (36 bp):
TTTTTAAAAAATTCTAAAATTTTATATAATTAAATA
Found at i:1438961 original size:6 final size:6
Alignment explanation
Indices: 1438947--1438980 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
1438937 AACAATAAAC
*
1438947 TGGGGA TGGGTA TGGGTA TGGGTA TGGGTA TGGG
1 TGGGTA TGGGTA TGGGTA TGGGTA TGGGTA TGGG
1438981 ACTCGAACCT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.15, C:0.00, G:0.56, T:0.29
Consensus pattern (6 bp):
TGGGTA
Found at i:1440813 original size:21 final size:21
Alignment explanation
Indices: 1440789--1440831 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1440779 TTTTTATATA
1440789 TATTATATTATATTATATTTT
1 TATTATATTATATTATATTTT
* * *
1440810 TATTTTATTTTATTTTATTTT
1 TATTATATTATATTATATTTT
1440831 T
1 T
1440832 TATTTTCAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (21 bp):
TATTATATTATATTATATTTT
Found at i:1444261 original size:31 final size:31
Alignment explanation
Indices: 1444184--1444262 Score: 140
Period size: 31 Copynumber: 2.5 Consensus size: 31
1444174 TAGTTGAAGT
* *
1444184 TATTTTATTTATTTTATTTTTGTTGATATAA
1 TATTTTATTTATTTTCTTTTTGTTGATAGAA
1444215 TATTTTATTTATTTTCTTTTTGTTGATAGAA
1 TATTTTATTTATTTTCTTTTTGTTGATAGAA
1444246 TATTTTATTTATTTTCT
1 TATTTTATTTATTTTCT
1444263 CTCTCTCTCT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 46 1.00
ACGTcount: A:0.23, C:0.03, G:0.06, T:0.68
Consensus pattern (31 bp):
TATTTTATTTATTTTCTTTTTGTTGATAGAA
Found at i:1450143 original size:60 final size:60
Alignment explanation
Indices: 1450031--1450146 Score: 162
Period size: 60 Copynumber: 1.9 Consensus size: 60
1450021 ATAGTCGGGT
* *
1450031 GATCATTTTGTAACTTTTAATAGTCGAGAGACTTAATAAAGCAACATTCTATAGTCAAAA
1 GATCATTTTGTAACTTTTAATAGTCGAGAGACTTAATAAAACAACATCCTATAGTCAAAA
* * * *
1450091 GATCATTTTGTAACTTTTAATGGT-GAAGGGACTTAATAAAATAATATCCTATAGTC
1 GATCATTTTGTAACTTTTAATAGTCG-AGAGACTTAATAAAACAACATCCTATAGTC
1450147 GAGGGACCAT
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
59 1 0.02
60 48 0.98
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.35
Consensus pattern (60 bp):
GATCATTTTGTAACTTTTAATAGTCGAGAGACTTAATAAAACAACATCCTATAGTCAAAA
Found at i:1450158 original size:60 final size:60
Alignment explanation
Indices: 1450021--1450167 Score: 156
Period size: 60 Copynumber: 2.5 Consensus size: 60
1450011 AATATAATGA
* *
1450021 ATAGTCG-GGTGATCATTTTGTAACTTTTAATAGTCGAGAGACTTAATAAAGCAACATTCT
1 ATAGTCGAGG-GATCATTTTGTAACTTTTAATAGTCGAGAGACTTAATAAAACAACATCCT
* ** * * * *
1450081 ATAGTCAAAAGATCATTTTGTAACTTTTAATGGT-GAAGGGACTTAATAAAATAATATCCT
1 ATAGTCGAGGGATCATTTTGTAACTTTTAATAGTCG-AGAGACTTAATAAAACAACATCCT
*
1450141 ATAGTCGAGGGACCATTTTTGT-ACTTT
1 ATAGTCGAGGGATCA-TTTTGTAACTTT
1450168 ACCCATAAAA
Statistics
Matches: 71, Mismatches: 13, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
59 1 0.01
60 64 0.90
61 6 0.08
ACGTcount: A:0.34, C:0.12, G:0.18, T:0.36
Consensus pattern (60 bp):
ATAGTCGAGGGATCATTTTGTAACTTTTAATAGTCGAGAGACTTAATAAAACAACATCCT
Found at i:1454527 original size:41 final size:41
Alignment explanation
Indices: 1454482--1454744 Score: 422
Period size: 41 Copynumber: 6.4 Consensus size: 41
1454472 ATTCGCGTTG
1454482 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
* **
1454523 CATTTCGCGTTGCGATAGTCT-ACAGCCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGT-TGAAAATCGCGTTGCGATTTTC
*
1454564 CATTTCGCGTTGCGATAGTTTAAAATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
* *
1454605 CATTTCGCGTTGCGATAGTCT-ACAGTCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGT-TGAAAATCGCGTTGCGATTTTC
*
1454646 CGTTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
1454687 CATTTGCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
1 CATTT-CGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
1454729 CATTTCGCGTTGCGAT
1 CATTTCGCGTTGCGAT
1454745 TTTCCGTTTC
Statistics
Matches: 205, Mismatches: 12, Indels: 10
0.90 0.05 0.04
Matches are distributed among these distances:
40 2 0.01
41 160 0.78
42 43 0.21
ACGTcount: A:0.17, C:0.22, G:0.25, T:0.37
Consensus pattern (41 bp):
CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
Found at i:1454675 original size:103 final size:103
Alignment explanation
Indices: 1454487--1454767 Score: 243
Period size: 103 Copynumber: 2.7 Consensus size: 103
1454477 CGTTGCATTT
* * * * * * *
1454487 CGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAG--CC
1 CGCGTTGCGATAGTTCAAAATCGCGTTGCGATTCTACATGTCGCGTTGCGAT--T-TTCCGTTTC
* ** **
1454550 GCGTTGCGAT-TTTCCATTTCGCGTTGCGATAGTTT-AAAAT-
63 GCGTTGCGATAGTTGAAAATCGCGTTGCGAT--TTTCAAAATG
* * **
1454590 CGCGTTGCGAT-TTTCCATTTCGCGTTGCGATAGTCTACA-GTCGCGTTGCGATTTTCCGTTTCG
1 CGCGTTGCGATAGTTCAAAATCGCGTTGCGAT--TCTACATGTCGCGTTGCGATTTTCCGTTTCG
* **
1454653 CGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTG
64 CGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCAAAATG
* * * *
1454693 CGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATTTTCCGTTTCGCG
1 CGCGTTGCGATAGTTCAAAATCGCGTTGCGATTCTACATGTCGCGTTGCGATTTTCCGTTTCGCG
1454758 TTGCGATAGT
66 TTGCGATAGT
1454768 CTACAGTTGT
Statistics
Matches: 142, Mismatches: 27, Indels: 18
0.76 0.14 0.10
Matches are distributed among these distances:
100 3 0.02
101 4 0.03
102 32 0.23
103 84 0.59
104 19 0.13
ACGTcount: A:0.16, C:0.22, G:0.25, T:0.37
Consensus pattern (103 bp):
CGCGTTGCGATAGTTCAAAATCGCGTTGCGATTCTACATGTCGCGTTGCGATTTTCCGTTTCGCG
TTGCGATAGTTGAAAATCGCGTTGCGATTTTCAAAATG
Found at i:1454782 original size:62 final size:60
Alignment explanation
Indices: 1454549--1454767 Score: 235
Period size: 62 Copynumber: 3.6 Consensus size: 60
1454539 AGTCTACAGC
1454549 CGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTTAAAATCGCGTTGCGATTTTCCATTT
1 CGCGTTGCGATTTTCCATTTCGCGTTGCGATAG-TTAAAATCGCGTTGCGATTTTCCATTT
* * * * **** * ** **
1454610 CGCGTTGCGATAGTCTACA-GTCGCGTTGCGAT-TTTCCGTTTCGCGTTGCGATAGTTGAAAAT
1 CGCGTTGCGAT--TTTCCATTTCGCGTTGCGATAGTT-AAAATCGCGTTGCGAT-TTTCCATTT
1454672 CGCGTTGCGATTTTCCATTTGCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTT
1 CGCGTTGCGATTTTCCATTT-CGCGTTGCGATAGTT-AAAATCGCGTTGCGATTTTCCATTT
*
1454734 CGCGTTGCGATTTTCCGTTTCGCGTTGCGATAGT
1 CGCGTTGCGATTTTCCATTTCGCGTTGCGATAGT
1454768 CTACAGTTGT
Statistics
Matches: 123, Mismatches: 28, Indels: 14
0.75 0.17 0.08
Matches are distributed among these distances:
60 6 0.05
61 38 0.31
62 61 0.50
63 18 0.15
ACGTcount: A:0.16, C:0.21, G:0.25, T:0.38
Consensus pattern (60 bp):
CGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTAAAATCGCGTTGCGATTTTCCATTT
Found at i:1454820 original size:20 final size:20
Alignment explanation
Indices: 1454795--1454919 Score: 108
Period size: 20 Copynumber: 6.2 Consensus size: 20
1454785 ATTTTCAACT
*
1454795 ATCGCAACACGAAATGAAAA
1 ATCGCAACGCGAAATGAAAA
* *
1454815 ATCGCAACGCGAAACGGAAA
1 ATCGCAACGCGAAATGAAAA
* **
1454835 ATCGCAACGCG-ACTGTAGACT
1 ATCGCAACGCGAAATG-A-AAA
*
1454856 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGAAAA
** * **
1454876 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGA-AATGAAAA
1454897 ATCGCAACGCGAAATGAAAA
1 ATCGCAACGCGAAATGAAAA
1454917 ATC
1 ATC
1454920 ACTTGCGATG
Statistics
Matches: 78, Mismatches: 23, Indels: 8
0.72 0.21 0.07
Matches are distributed among these distances:
19 2 0.03
20 47 0.60
21 26 0.33
22 3 0.04
ACGTcount: A:0.42, C:0.24, G:0.20, T:0.14
Consensus pattern (20 bp):
ATCGCAACGCGAAATGAAAA
Found at i:1454863 original size:41 final size:41
Alignment explanation
Indices: 1454815--1455033 Score: 162
Period size: 41 Copynumber: 5.4 Consensus size: 41
1454805 GAAATGAAAA
*
1454815 ATCGCAACGCGAAACGGAAAATCGCAACGCGACTGT-AGACT
1 ATCGCAACGCGAAATGGAAAATCGCAACGCGACTGTCA-ACT
* *
1454856 ATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGGAAAATCGCAACGCGACTGTCAACT
* * ** ** *
1454897 ATCGCAACGCGAAATGAAAAATCAC-TTGCGA-TGATGGA-G
1 ATCGCAACGCGAAATGGAAAATCGCAACGCGACTG-TCAACT
*** * ** * *
1454936 ATCGCGTTGCG-ATTTCAACTATCGCAACGCGATCT-CCAACT
1 ATCGCAACGCGAAATGGAA-AATCGCAACGCGA-CTGTCAACT
* * *
1454977 ATCGCAACGCGAAATGGAAAAACGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGGAAAATCGCAACGCGACTGTCAACT
*
1455018 ATCGCAATGCGAAATG
1 ATCGCAACGCGAAATG
1455034 CAACGTGAAT
Statistics
Matches: 133, Mismatches: 36, Indels: 18
0.71 0.19 0.10
Matches are distributed among these distances:
38 4 0.03
39 13 0.10
40 12 0.09
41 98 0.74
42 6 0.05
ACGTcount: A:0.35, C:0.25, G:0.21, T:0.19
Consensus pattern (41 bp):
ATCGCAACGCGAAATGGAAAATCGCAACGCGACTGTCAACT
Found at i:1455037 original size:21 final size:21
Alignment explanation
Indices: 1454951--1455037 Score: 77
Period size: 21 Copynumber: 4.2 Consensus size: 21
1454941 GTTGCGATTT
** *
1454951 CAACTATCGCAACGCGATCTC
1 CAACTATCGCAACGCGAAATG
1454972 CAACTATCGCAACGCGAAATG
1 CAACTATCGCAACGCGAAATG
* * * ** *
1454993 GAA-AAACGCAACGCGATTTT
1 CAACTATCGCAACGCGAAATG
*
1455013 CAACTATCGCAATGCGAAATG
1 CAACTATCGCAACGCGAAATG
1455034 CAAC
1 CAAC
1455038 GTGAATTTGC
Statistics
Matches: 49, Mismatches: 16, Indels: 2
0.73 0.24 0.03
Matches are distributed among these distances:
20 14 0.29
21 35 0.71
ACGTcount: A:0.37, C:0.29, G:0.17, T:0.17
Consensus pattern (21 bp):
CAACTATCGCAACGCGAAATG
Found at i:1455089 original size:121 final size:121
Alignment explanation
Indices: 1454835--1455072 Score: 318
Period size: 121 Copynumber: 2.0 Consensus size: 121
1454825 GAAACGGAAA
** *
1454835 ATCGCAACGCGA-CTGTAGACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACTAT
1 ATCGCAACGCGATCTCCA-ACTATCGCAACGCGAAATGGAAAAACGCAACGCGATTTTCAACTAT
* ** * *
1454899 CGCAACGCGAAATGAAAAATCACTTGCGATGATGGAGATCGCGTTGCGATTTCAACT
65 CGCAACGCGAAATGAAAAATAACTTGCGATGATGGAGATCGCAATGCGAATTCAACG
1454956 ATCGCAACGCGATCTCCAACTATCGCAACGCGAAATGGAAAAACGCAACGCGATTTTCAACTATC
1 ATCGCAACGCGATCTCCAACTATCGCAACGCGAAATGGAAAAACGCAACGCGATTTTCAACTATC
* * ** *
1455021 GCAATGCGAAATGCAACGTGAATTTGCGAT-AGTGGAGATCGCAATGCGAATT
66 GCAACGCGAAATGAAAAAT-AACTTGCGATGA-TGGAGATCGCAATGCGAATT
1455073 AGAGATCGCA
Statistics
Matches: 102, Mismatches: 12, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
121 74 0.73
122 28 0.27
ACGTcount: A:0.34, C:0.23, G:0.22, T:0.21
Consensus pattern (121 bp):
ATCGCAACGCGATCTCCAACTATCGCAACGCGAAATGGAAAAACGCAACGCGATTTTCAACTATC
GCAACGCGAAATGAAAAATAACTTGCGATGATGGAGATCGCAATGCGAATTCAACG
Found at i:1457207 original size:24 final size:26
Alignment explanation
Indices: 1457174--1457234 Score: 81
Period size: 26 Copynumber: 2.4 Consensus size: 26
1457164 GAATACATTT
* *
1457174 TATATATATTTAAAAT-TGT-AATCAA
1 TATA-ATATTTAAAATAAGTAAATAAA
1457199 TATAATATTTAAAATAAGTAAATAAA
1 TATAATATTTAAAATAAGTAAATAAA
1457225 TATAATATTT
1 TATAATATTT
1457235 TTAAACTAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
24 11 0.34
25 6 0.19
26 15 0.47
ACGTcount: A:0.52, C:0.02, G:0.03, T:0.43
Consensus pattern (26 bp):
TATAATATTTAAAATAAGTAAATAAA
Found at i:1457405 original size:24 final size:25
Alignment explanation
Indices: 1457352--1457449 Score: 67
Period size: 29 Copynumber: 3.7 Consensus size: 25
1457342 TAAACCAATA
1457352 TAATA-TTTAAAATAAAACTAAGTT
1 TAATATTTTAAAATAAAACTAAGTT
* *
1457376 TTATATTTTAAACTAAAA-TAA-TT
1 TAATATTTTAAAATAAAACTAAGTT
1457399 TCAATATAATATTTAAAATAATAACAATAAGTT
1 T--A-AT-AT-TTTAAAATAA-AAC--TAAGTT
*
1457432 TAATATTTTTAAACTAAA
1 TAATA-TTTTAAAATAAA
1457450 TTTAATATAT
Statistics
Matches: 57, Mismatches: 5, Indels: 20
0.70 0.06 0.24
Matches are distributed among these distances:
23 3 0.05
24 7 0.12
25 11 0.19
26 2 0.04
27 2 0.04
28 10 0.18
29 12 0.21
30 3 0.05
31 1 0.02
32 3 0.05
33 3 0.05
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.41
Consensus pattern (25 bp):
TAATATTTTAAAATAAAACTAAGTT
Found at i:1457534 original size:24 final size:23
Alignment explanation
Indices: 1457486--1457538 Score: 72
Period size: 24 Copynumber: 2.3 Consensus size: 23
1457476 TGGAAAAATA
*
1457486 TATTTAAAAATATTGAATTATTT
1 TATTTAAAAATATTAAATTATTT
1457509 TAGTTTAAAAATATTAAATT-TATT
1 TA-TTTAAAAATATTAAATTAT-TT
1457533 TATTTA
1 TATTTA
1457539 TTTTAAATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
23 7 0.26
24 20 0.74
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (23 bp):
TATTTAAAAATATTAAATTATTT
Found at i:1461457 original size:24 final size:25
Alignment explanation
Indices: 1461407--1461458 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
1461397 ACTTTTATCC
* *
1461407 TCTAAAATTTTATAAATTTATTCTT
1 TCTAAAATTATATAAATTTAATCTT
*
1461432 TCTAAAATTATATAATTTTAAT-TT
1 TCTAAAATTATATAAATTTAATCTT
1461456 TCT
1 TCT
1461459 TAATATAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
24 5 0.21
25 19 0.79
ACGTcount: A:0.37, C:0.08, G:0.00, T:0.56
Consensus pattern (25 bp):
TCTAAAATTATATAAATTTAATCTT
Found at i:1464263 original size:22 final size:22
Alignment explanation
Indices: 1464231--1464312 Score: 92
Period size: 22 Copynumber: 3.7 Consensus size: 22
1464221 GAAAATATTC
* *
1464231 GTTTAATGTTTCTTTAGTGTTT
1 GTTTAACGTTTGTTTAGTGTTT
** *
1464253 GTTTAACGTTTGTTTAACGTTC
1 GTTTAACGTTTGTTTAGTGTTT
*
1464275 GTTTAATGTTTGTTTAGTGTTT
1 GTTTAACGTTTGTTTAGTGTTT
* *
1464297 GTTTAGCGTTCGTTTA
1 GTTTAACGTTTGTTTA
1464313 TACATTCAAT
Statistics
Matches: 48, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
22 48 1.00
ACGTcount: A:0.15, C:0.07, G:0.21, T:0.57
Consensus pattern (22 bp):
GTTTAACGTTTGTTTAGTGTTT
Found at i:1464268 original size:33 final size:33
Alignment explanation
Indices: 1464243--1464312 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
1464233 TTAATGTTTC
*
1464243 TTTAGTGTTTGTTTAACGTTTGTTTAACGTTCG
1 TTTAATGTTTGTTTAACGTTTGTTTAACGTTCG
** *
1464276 TTTAATGTTTGTTTAGTGTTTGTTTAGCGTTCG
1 TTTAATGTTTGTTTAACGTTTGTTTAACGTTCG
1464309 TTTA
1 TTTA
1464313 TACATTCAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.14, C:0.07, G:0.21, T:0.57
Consensus pattern (33 bp):
TTTAATGTTTGTTTAACGTTTGTTTAACGTTCG
Found at i:1464302 original size:11 final size:11
Alignment explanation
Indices: 1464231--1464301 Score: 88
Period size: 11 Copynumber: 6.5 Consensus size: 11
1464221 GAAAATATTC
1464231 GTTTAATGTTT
1 GTTTAATGTTT
* *
1464242 CTTTAGTGTTT
1 GTTTAATGTTT
*
1464253 GTTTAACGTTT
1 GTTTAATGTTT
* *
1464264 GTTTAACGTTC
1 GTTTAATGTTT
1464275 GTTTAATGTTT
1 GTTTAATGTTT
*
1464286 GTTTAGTGTTT
1 GTTTAATGTTT
1464297 GTTTA
1 GTTTA
1464302 GCGTTCGTTT
Statistics
Matches: 51, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
11 51 1.00
ACGTcount: A:0.15, C:0.06, G:0.20, T:0.59
Consensus pattern (11 bp):
GTTTAATGTTT
Found at i:1464311 original size:11 final size:11
Alignment explanation
Indices: 1464249--1464312 Score: 74
Period size: 11 Copynumber: 5.8 Consensus size: 11
1464239 TTTCTTTAGT
1464249 GTTTGTTTAAC
1 GTTTGTTTAAC
1464260 GTTTGTTTAAC
1 GTTTGTTTAAC
* *
1464271 GTTCGTTTAAT
1 GTTTGTTTAAC
**
1464282 GTTTGTTTAGT
1 GTTTGTTTAAC
*
1464293 GTTTGTTTAGC
1 GTTTGTTTAAC
*
1464304 GTTCGTTTA
1 GTTTGTTTA
1464313 TACATTCAAT
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 47 1.00
ACGTcount: A:0.14, C:0.08, G:0.22, T:0.56
Consensus pattern (11 bp):
GTTTGTTTAAC
Found at i:1470078 original size:32 final size:32
Alignment explanation
Indices: 1470034--1470094 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 32
1470024 CAACTCTAAT
* **
1470034 TATACAATATACTCTAGTTATGATATTAAAAC
1 TATACAACATACTCTAAATATGATATTAAAAC
*
1470066 TATACAACATACTTTAAATATGATATTAA
1 TATACAACATACTCTAAATATGATATTAA
1470095 GGGTCTGTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.46, C:0.11, G:0.05, T:0.38
Consensus pattern (32 bp):
TATACAACATACTCTAAATATGATATTAAAAC
Found at i:1470142 original size:14 final size:14
Alignment explanation
Indices: 1470123--1470181 Score: 64
Period size: 14 Copynumber: 4.1 Consensus size: 14
1470113 GTAATTGATT
*
1470123 TTCTGGAAATTGAA
1 TTCTGGAAAATGAA
*
1470137 TTCTGGAAAATAAA
1 TTCTGGAAAATGAA
* **
1470151 TTAATGGAATTTGAA
1 TT-CTGGAAAATGAA
1470166 TTCTGGAAAATGAA
1 TTCTGGAAAATGAA
1470180 TT
1 TT
1470182 ACATTTTTTG
Statistics
Matches: 35, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
14 25 0.71
15 10 0.29
ACGTcount: A:0.41, C:0.05, G:0.19, T:0.36
Consensus pattern (14 bp):
TTCTGGAAAATGAA
Found at i:1470168 original size:29 final size:29
Alignment explanation
Indices: 1470126--1470182 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
1470116 ATTGATTTTC
1470126 TGGAAATTGAATTCTGGAAAATAAATTAA
1 TGGAAATTGAATTCTGGAAAATAAATTAA
* *
1470155 TGGAATTTGAATTCTGGAAAATGAATTA
1 TGGAAATTGAATTCTGGAAAATAAATTA
1470183 CATTTTTTGG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.44, C:0.04, G:0.19, T:0.33
Consensus pattern (29 bp):
TGGAAATTGAATTCTGGAAAATAAATTAA
Found at i:1470483 original size:31 final size:29
Alignment explanation
Indices: 1470415--1470484 Score: 70
Period size: 31 Copynumber: 2.2 Consensus size: 29
1470405 AATATTATTT
*
1470415 TTATAATTTTATTAATAAAAATATTAATAT
1 TTAT-ATTTTATTAATAAAAATATTAATAA
1470445 TGGTATATTTTATTGAAATAAAAATATT-ATAAA
1 T--TATATTTTATT--AATAAAAATATTAAT-AA
1470478 TTATATT
1 TTATATT
1470485 AATTATTTAT
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
30 1 0.03
31 14 0.41
32 5 0.15
33 14 0.41
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (29 bp):
TTATATTTTATTAATAAAAATATTAATAA
Found at i:1470585 original size:28 final size:29
Alignment explanation
Indices: 1470554--1470637 Score: 84
Period size: 30 Copynumber: 2.8 Consensus size: 29
1470544 TAAATATCTT
*
1470554 TATTAAAATTATTAGATTATTA-TATTAA
1 TATTAAAATTAATAGATTATTATTATTAA
*
1470582 TATTAAATATATAATATATTATTATTATTAA
1 TATTAAA-AT-TAATAGATTATTATTATTAA
1470613 TAATTAATAATTTAATA-A-TATTATT
1 T-ATTAA-AA-TTAATAGATTATTATT
1470638 TCTATGAATT
Statistics
Matches: 48, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
28 7 0.15
29 2 0.04
30 18 0.38
31 8 0.17
32 11 0.23
33 2 0.04
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (29 bp):
TATTAAAATTAATAGATTATTATTATTAA
Found at i:1470605 original size:30 final size:33
Alignment explanation
Indices: 1470569--1470661 Score: 97
Period size: 33 Copynumber: 2.9 Consensus size: 33
1470559 AAATTATTAG
1470569 ATTATTA-TATTAAT-ATTAA-ATATATAAT-AT
1 ATTATTATTATTAATAATTAATA-ATATAATAAT
*
1470599 ATTATTATTATTAATAATTAATAATTTAATAAT
1 ATTATTATTATTAATAATTAATAATATAATAAT
* *
1470632 ATTATT-TCTATGAATTAATAAATAATATAA
1 ATTATTAT-TATTAA-TAATTAATAATATAA
1470662 ATTTTATTAA
Statistics
Matches: 53, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
30 7 0.13
31 7 0.13
32 12 0.23
33 14 0.26
34 13 0.25
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (33 bp):
ATTATTATTATTAATAATTAATAATATAATAAT
Found at i:1476697 original size:12 final size:12
Alignment explanation
Indices: 1476680--1476709 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
1476670 AAATAGCAGT
1476680 GATGAAGCTTGA
1 GATGAAGCTTGA
1476692 GATGAAGCTTGA
1 GATGAAGCTTGA
1476704 GATGAA
1 GATGAA
1476710 AACTGATTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.37, C:0.07, G:0.33, T:0.23
Consensus pattern (12 bp):
GATGAAGCTTGA
Found at i:1481793 original size:24 final size:24
Alignment explanation
Indices: 1481761--1481808 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
1481751 TTAAAATTCG
1481761 ACCCTACTTGATTCGAATAAGTAC
1 ACCCTACTTGATTCGAATAAGTAC
1481785 ACCCTACTTGATTCGAATAAGTAC
1 ACCCTACTTGATTCGAATAAGTAC
1481809 GCATTAAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.33, C:0.25, G:0.12, T:0.29
Consensus pattern (24 bp):
ACCCTACTTGATTCGAATAAGTAC
Found at i:1489262 original size:27 final size:27
Alignment explanation
Indices: 1489227--1489287 Score: 90
Period size: 27 Copynumber: 2.3 Consensus size: 27
1489217 TTGCCACCAA
1489227 GCTTA-CTCACCTCCCAGACCGCATCG
1 GCTTACCTCACCTCCCAGACCGCATCG
*
1489253 GCTTACCTCACCTCCCAGACTGCATCG
1 GCTTACCTCACCTCCCAGACCGCATCG
*
1489280 ACTT-CCTC
1 GCTTACCTC
1489288 TCCAATTTCA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
26 9 0.28
27 23 0.72
ACGTcount: A:0.18, C:0.46, G:0.13, T:0.23
Consensus pattern (27 bp):
GCTTACCTCACCTCCCAGACCGCATCG
Found at i:1489934 original size:61 final size:61
Alignment explanation
Indices: 1489859--1489980 Score: 217
Period size: 61 Copynumber: 2.0 Consensus size: 61
1489849 TCTTTTTAAC
* *
1489859 CTAGGATTTGCATATGCCCAATAAGGAAAGTTGGTACACGTATTTACTTGCTGATCAATTT
1 CTAGGATTTGCATATGACCAATAAGGAAAGTTGGTACACATATTTACTTGCTGATCAATTT
*
1489920 CTAGGATTTGCATATGACCAATAAGGAAAGTTGGTCCACATATTTACTTGCTGATCAATTT
1 CTAGGATTTGCATATGACCAATAAGGAAAGTTGGTACACATATTTACTTGCTGATCAATTT
1489981 AATTAATATT
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
61 58 1.00
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.34
Consensus pattern (61 bp):
CTAGGATTTGCATATGACCAATAAGGAAAGTTGGTACACATATTTACTTGCTGATCAATTT
Found at i:1495741 original size:43 final size:43
Alignment explanation
Indices: 1495694--1495783 Score: 112
Period size: 43 Copynumber: 2.1 Consensus size: 43
1495684 TAAAATGATT
* * *
1495694 AATTAGGAGAC-TCAATTATAAATGTA-AAATGTGAGATTAAAAA
1 AATTAGGAG-CTTCAATTATAAATATAGAAA-GTAAAATTAAAAA
*
1495737 AATTAGGTGCTTCAATTATAAATATAGAAAGTAAAATTAAAAA
1 AATTAGGAGCTTCAATTATAAATATAGAAAGTAAAATTAAAAA
1495780 AATT
1 AATT
1495784 GATATTGAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
42 1 0.02
43 37 0.90
44 3 0.07
ACGTcount: A:0.52, C:0.04, G:0.13, T:0.30
Consensus pattern (43 bp):
AATTAGGAGCTTCAATTATAAATATAGAAAGTAAAATTAAAAA
Found at i:1502416 original size:24 final size:23
Alignment explanation
Indices: 1502389--1502443 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 23
1502379 CTATGATACA
* *
1502389 AAATAATATTATTTTTATAATCAT
1 AAATAATATTAATTGTAT-ATCAT
* *
1502413 AAATAAAATTAATTGTATATTAT
1 AAATAATATTAATTGTATATCAT
1502436 AAATAATA
1 AAATAATA
1502444 AATCTTCAGT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
23 11 0.42
24 15 0.58
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (23 bp):
AAATAATATTAATTGTATATCAT
Found at i:1504063 original size:32 final size:32
Alignment explanation
Indices: 1504027--1504097 Score: 115
Period size: 32 Copynumber: 2.2 Consensus size: 32
1504017 ATAGTGACCG
1504027 TTATATAACGATAATAATATTATCGGAAACCA
1 TTATATAACGATAATAATATTATCGGAAACCA
* **
1504059 TTATATAACGATAATAATATTGTCGGAAACTG
1 TTATATAACGATAATAATATTATCGGAAACCA
1504091 TTATATA
1 TTATATA
1504098 TCTACTATAT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.44, C:0.10, G:0.11, T:0.35
Consensus pattern (32 bp):
TTATATAACGATAATAATATTATCGGAAACCA
Found at i:1507735 original size:60 final size:60
Alignment explanation
Indices: 1507601--1507747 Score: 147
Period size: 60 Copynumber: 2.5 Consensus size: 60
1507591 AATATAATGA
* * *
1507601 ATAGTCG-GGTGATCATTTTGTAACTTTTAATAGTCGAGAGACTTAATAAAGCAACATTCT
1 ATAGTCGAGG-GACCATTTTGTAACTTTTAATAGTCGAGAGACTTAATAAAACAACATCCT
* ** * * * **
1507661 ATAGTCAAAAGACCATTTTGTAACTTTTAATGGT-GAAGGGACTTAATAAAATAGTATCCT
1 ATAGTCGAGGGACCATTTTGTAACTTTTAATAGTCG-AGAGACTTAATAAAACAACATCCT
1507721 ATAGTCGAGGGACCATTTTTGT-ACTTT
1 ATAGTCGAGGGACCA-TTTTGTAACTTT
1507748 ACCCATAAAA
Statistics
Matches: 70, Mismatches: 14, Indels: 6
0.78 0.16 0.07
Matches are distributed among these distances:
59 1 0.01
60 63 0.90
61 6 0.09
ACGTcount: A:0.33, C:0.13, G:0.18, T:0.35
Consensus pattern (60 bp):
ATAGTCGAGGGACCATTTTGTAACTTTTAATAGTCGAGAGACTTAATAAAACAACATCCT
Found at i:1510869 original size:29 final size:29
Alignment explanation
Indices: 1510836--1510903 Score: 118
Period size: 29 Copynumber: 2.3 Consensus size: 29
1510826 AACATAGGTT
*
1510836 TTCATGGAGAATCTAATTTTATTTTGTGG
1 TTCATGGAGAATCTAATTTTATTTTGTGA
1510865 TTCATGGAGAATCTAATTTTATTTTGTGA
1 TTCATGGAGAATCTAATTTTATTTTGTGA
*
1510894 TTAATGGAGA
1 TTCATGGAGA
1510904 TATCACGTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.28, C:0.06, G:0.21, T:0.46
Consensus pattern (29 bp):
TTCATGGAGAATCTAATTTTATTTTGTGA
Found at i:1512095 original size:21 final size:21
Alignment explanation
Indices: 1512075--1512299 Score: 158
Period size: 21 Copynumber: 10.9 Consensus size: 21
1512065 ATTCGCGTTG
*
1512075 CATTTCGCGTTGCGATAGTTG
1 CATTTCGCGTTGCGATAGTTC
* ** *
1512096 AAAATCGCGTTGCGAT-TTTC
1 CATTTCGCGTTGCGATAGTTC
1512116 CATTTCGCGTTGCGATAG-TC
1 CATTTCGCGTTGCGATAGTTC
* * *
1512136 TATAGTCGCGTTGCGAT-TTTC
1 CAT-TTCGCGTTGCGATAGTTC
* *
1512157 CATTTCACGTTGCGATAGTCTA
1 CATTTCGCGTTGCGATAGT-TC
* *
1512179 CAGTT-GCGTTGCGAT-TTTC
1 CATTTCGCGTTGCGATAGTTC
* *
1512198 CGTTTCGCGTTGCGATAGTTG
1 CATTTCGCGTTGCGATAGTTC
* ** *
1512219 AAAATCGCGTTGCGAT-TTTC
1 CATTTCGCGTTGCGATAGTTC
*
1512239 CATTTGCGCGTTGCGATAGTTG
1 CATTT-CGCGTTGCGATAGTTC
* ** *
1512261 AAAATCGCGTTGCGAT-TTTC
1 CATTTCGCGTTGCGATAGTTC
*
1512281 CGTTTCGCGTTGCGATAGT
1 CATTTCGCGTTGCGATAGT
1512300 CTACAGTTGT
Statistics
Matches: 148, Mismatches: 46, Indels: 20
0.69 0.21 0.09
Matches are distributed among these distances:
19 4 0.03
20 59 0.40
21 76 0.51
22 9 0.06
ACGTcount: A:0.17, C:0.20, G:0.25, T:0.37
Consensus pattern (21 bp):
CATTTCGCGTTGCGATAGTTC
Found at i:1512120 original size:41 final size:41
Alignment explanation
Indices: 1512075--1512299 Score: 337
Period size: 41 Copynumber: 5.5 Consensus size: 41
1512065 ATTCGCGTTG
1512075 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
* *
1512116 CATTTCGCGTTGCGATAGTCT-ATAGTCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGT-TGAAAATCGCGTTGCGATTTTC
* * * *
1512157 CATTTCACGTTGCGATAGTCT-ACAGTTGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGT-TGAAAATCGCGTTGCGATTTTC
*
1512198 CGTTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
1512239 CATTTGCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
1 CATTT-CGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
*
1512281 CGTTTCGCGTTGCGATAGT
1 CATTTCGCGTTGCGATAGT
1512300 CTACAGTTGT
Statistics
Matches: 169, Mismatches: 12, Indels: 6
0.90 0.06 0.03
Matches are distributed among these distances:
40 1 0.01
41 127 0.75
42 41 0.24
ACGTcount: A:0.17, C:0.20, G:0.25, T:0.37
Consensus pattern (41 bp):
CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
Found at i:1512345 original size:124 final size:123
Alignment explanation
Indices: 1512087--1512351 Score: 340
Period size: 124 Copynumber: 2.1 Consensus size: 123
1512077 TTTCGCGTTG
* * *
1512087 CGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTATAGTCGCGTTGCGA
1 CGATAGATGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTAAAATCGCGTTGCGA
* ****
1512152 TTTTCCATTTCACGTTGCGATAGTCTACAGTTGCGTTGCGATTTTCCGTTTCGCGTTG
66 TTTTCCATTTCACGTTGCGATAGTCTACAGTTGCGTTGCGATTTTCCGTATCGCAACA
*
1512210 CGATAGTTGAAAATCGCGTTGCGATTTTCCATTTGCGCGTTGCGATAGT-TGAAAATCGCGTTGC
1 CGATAGATGAAAATCGCGTTGCGATTTTCCATTT-CGCGTTGCGATAGTCT-AAAATCGCGTTGC
* * *
1512274 GATTTTCCGTTTCGCGTTGCGATAGTCTACAGTTGTCGTTGTGATTTTCAAC-TATCGCAACA
64 GATTTTCCATTTCACGTTGCGATAGTCTACAGTTG-CGTTGCGATTTTC--CGTATCGCAACA
1512336 CGA-A-ATGAAAAATCGC
1 CGATAGATG-AAAATCGC
1512352 AACGCGATTT
Statistics
Matches: 125, Mismatches: 11, Indels: 10
0.86 0.08 0.07
Matches are distributed among these distances:
123 35 0.28
124 60 0.48
125 21 0.17
126 8 0.06
127 1 0.01
ACGTcount: A:0.20, C:0.20, G:0.24, T:0.35
Consensus pattern (123 bp):
CGATAGATGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTAAAATCGCGTTGCGA
TTTTCCATTTCACGTTGCGATAGTCTACAGTTGCGTTGCGATTTTCCGTATCGCAACA
Found at i:1512352 original size:20 final size:20
Alignment explanation
Indices: 1512327--1512451 Score: 97
Period size: 20 Copynumber: 6.2 Consensus size: 20
1512317 ATTTTCAACT
*
1512327 ATCGCAACACGAAATGAAAA
1 ATCGCAACGCGAAATGAAAA
** * **
1512347 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGA-AATGAAAA
* *
1512368 ATCGCAACGCGAAACGGAAA
1 ATCGCAACGCGAAATGAAAA
*
1512388 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGAAAA
** * **
1512408 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGA-AATGAAAA
*
1512429 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGAAAA
1512449 ATC
1 ATC
1512452 ACTTGCGATG
Statistics
Matches: 77, Mismatches: 26, Indels: 4
0.72 0.24 0.04
Matches are distributed among these distances:
20 48 0.62
21 29 0.38
ACGTcount: A:0.41, C:0.24, G:0.19, T:0.16
Consensus pattern (20 bp):
ATCGCAACGCGAAATGAAAA
Found at i:1512363 original size:41 final size:41
Alignment explanation
Indices: 1512316--1512399 Score: 141
Period size: 41 Copynumber: 2.0 Consensus size: 41
1512306 TTGTCGTTGT
*
1512316 GATTTTCAACTATCGCAACACGAAATGAAAAATCGCAACGC
1 GATTTTCAACTATCGCAACACGAAACGAAAAATCGCAACGC
* *
1512357 GATTTTCAACTATCGCAACGCGAAACGGAAAATCGCAACGC
1 GATTTTCAACTATCGCAACACGAAACGAAAAATCGCAACGC
1512398 GA
1 GA
1512400 AATGGAAAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.39, C:0.25, G:0.18, T:0.18
Consensus pattern (41 bp):
GATTTTCAACTATCGCAACACGAAACGAAAAATCGCAACGC
Found at i:1512403 original size:61 final size:61
Alignment explanation
Indices: 1512327--1512563 Score: 250
Period size: 61 Copynumber: 3.9 Consensus size: 61
1512317 ATTTTCAACT
*
1512327 ATCGCAACACGAAATGAAAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAACGGAAA
1 ATCGCAACGCGAAATGAAAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAACGGAAA
* *
1512388 ATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGAAAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAACGGAAA
* ** * * * *** * ** *
1512449 ATCAC-TTGCGATGATG-GAGATCGCGTTGCGA-TTTCAACTATCGCAACGCG-ATCTCCAACT
1 ATCGCAACGCGA-AATGAAAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAAC-GGAA-A
*
1512509 ATCGCAACGCGAAATGGAAAAA-CGCAACGCGATTTTCAACTATCGCAATGCGAAA
1 ATCGCAACGCGAAAT-GAAAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAA
1512564 TGCAACGTGA
Statistics
Matches: 140, Mismatches: 28, Indels: 14
0.77 0.15 0.08
Matches are distributed among these distances:
58 1 0.01
59 21 0.15
60 20 0.14
61 77 0.55
62 20 0.14
63 1 0.01
ACGTcount: A:0.37, C:0.24, G:0.20, T:0.19
Consensus pattern (61 bp):
ATCGCAACGCGAAATGAAAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAACGGAAA
Found at i:1512433 original size:41 final size:41
Alignment explanation
Indices: 1512388--1512565 Score: 155
Period size: 41 Copynumber: 4.4 Consensus size: 41
1512378 GAAACGGAAA
1512388 ATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACT
* ** ** ** *
1512429 ATCGCAACGCGAAATGGAAAATCAC-TTGCGATGATGGA-G
1 ATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACT
*** * ** * * *
1512468 ATCGCGTTGCG-ATTTCAACTATCGCAACGCGATCTCCAACT
1 ATCGCAACGCGAAATGGAA-AATCGCAACGCGATTTTCAACT
*
1512509 ATCGCAACGCGAAATGGAAAAACGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACT
*
1512550 ATCGCAATGCGAAATG
1 ATCGCAACGCGAAATG
1512566 CAACGTGAAT
Statistics
Matches: 98, Mismatches: 35, Indels: 8
0.70 0.25 0.06
Matches are distributed among these distances:
38 4 0.04
39 12 0.12
40 13 0.13
41 65 0.66
42 4 0.04
ACGTcount: A:0.34, C:0.24, G:0.21, T:0.20
Consensus pattern (41 bp):
ATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACT
Found at i:1512569 original size:21 final size:21
Alignment explanation
Indices: 1512483--1512569 Score: 77
Period size: 21 Copynumber: 4.2 Consensus size: 21
1512473 GTTGCGATTT
** *
1512483 CAACTATCGCAACGCGATCTC
1 CAACTATCGCAACGCGAAATG
1512504 CAACTATCGCAACGCGAAATG
1 CAACTATCGCAACGCGAAATG
* * * ** *
1512525 GAA-AAACGCAACGCGATTTT
1 CAACTATCGCAACGCGAAATG
*
1512545 CAACTATCGCAATGCGAAATG
1 CAACTATCGCAACGCGAAATG
1512566 CAAC
1 CAAC
1512570 GTGAATTTGT
Statistics
Matches: 49, Mismatches: 16, Indels: 2
0.73 0.24 0.03
Matches are distributed among these distances:
20 14 0.29
21 35 0.71
ACGTcount: A:0.37, C:0.29, G:0.17, T:0.17
Consensus pattern (21 bp):
CAACTATCGCAACGCGAAATG
Found at i:1514795 original size:24 final size:26
Alignment explanation
Indices: 1514762--1514822 Score: 81
Period size: 26 Copynumber: 2.4 Consensus size: 26
1514752 GAATACATTT
* *
1514762 TATATATATTTAAAAT-TGT-AATCAA
1 TATA-ATATTTAAAATAAGTAAATAAA
1514787 TATAATATTTAAAATAAGTAAATAAA
1 TATAATATTTAAAATAAGTAAATAAA
1514813 TATAATATTT
1 TATAATATTT
1514823 GTAAACTAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
24 11 0.34
25 6 0.19
26 15 0.47
ACGTcount: A:0.52, C:0.02, G:0.03, T:0.43
Consensus pattern (26 bp):
TATAATATTTAAAATAAGTAAATAAA
Found at i:1515139 original size:2 final size:2
Alignment explanation
Indices: 1515132--1515156 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1515122 ACAATTTTAA
1515132 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1515157 ATGTATTCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1519006 original size:23 final size:24
Alignment explanation
Indices: 1518980--1519031 Score: 61
Period size: 25 Copynumber: 2.2 Consensus size: 24
1518970 TTTATTAATA
* *
1518980 ATAAGTTCA-TTTTCTAAAATTTT
1 ATAAATTCATTTTTCTAAAATTAT
*
1519003 ATAAATTTATTTTTTCTAAAATTAT
1 ATAAATTCA-TTTTTCTAAAATTAT
1519028 ATAA
1 ATAA
1519032 TTTTAATTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 7 0.29
25 17 0.71
ACGTcount: A:0.40, C:0.06, G:0.02, T:0.52
Consensus pattern (24 bp):
ATAAATTCATTTTTCTAAAATTAT
Found at i:1519022 original size:25 final size:25
Alignment explanation
Indices: 1518989--1519041 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
1518979 AATAAGTTCA
* *
1518989 TTTTCTAAAATTTTATAAATTTATT
1 TTTTCTAAAATTATATAAATTTAAT
*
1519014 TTTTCTAAAATTATATAATTTTAAT
1 TTTTCTAAAATTATATAAATTTAAT
1519039 TTT
1 TTT
1519042 CTTAATATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (25 bp):
TTTTCTAAAATTATATAAATTTAAT
Found at i:1520164 original size:2 final size:2
Alignment explanation
Indices: 1520148--1520183 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
1520138 ATATAACATC
*
1520148 AT AT -T AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1520184 GGGATAAGAT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1521094 original size:2 final size:2
Alignment explanation
Indices: 1521087--1521113 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1521077 TCATGAGTAT
1521087 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1521114 TAATAATTCA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1521497 original size:11 final size:11
Alignment explanation
Indices: 1521474--1521513 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
1521464 CACGAAAATA
*
1521474 TTCGTTTAATG
1 TTCGTTTAGTG
*
1521485 TTTGTTTAGTG
1 TTCGTTTAGTG
*
1521496 TTCGTTTAGCG
1 TTCGTTTAGTG
1521507 TTCGTTT
1 TTCGTTT
1521514 TTACATTCAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.10, C:0.10, G:0.23, T:0.57
Consensus pattern (11 bp):
TTCGTTTAGTG
Found at i:1550052 original size:25 final size:24
Alignment explanation
Indices: 1550015--1550095 Score: 78
Period size: 24 Copynumber: 3.3 Consensus size: 24
1550005 TTAAATTCAT
1550015 AATATTTTATATATATTAACTTAAAA
1 AATATTTT-TATATATTAA-TTAAAA
* **
1550041 AATATTTTTATAT-TAAATTATTA
1 AATATTTTTATATATTAATTAAAA
1550064 AATATATTTTAT-TATTAATCT-AAA
1 AATAT-TTTTATATATTAAT-TAAAA
1550088 AATATTTT
1 AATATTTT
1550096 ATTTTTATTT
Statistics
Matches: 46, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
23 13 0.28
24 19 0.41
25 6 0.13
26 8 0.17
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (24 bp):
AATATTTTTATATATTAATTAAAA
Found at i:1550090 original size:24 final size:22
Alignment explanation
Indices: 1550026--1550095 Score: 70
Period size: 23 Copynumber: 3.0 Consensus size: 22
1550016 ATATTTTATA
*
1550026 TATATTAACTTAAAAAATATTTT
1 TATATTAAATT-AAAAATATTTT
*
1550049 TATATTAAATTATTAAATATATTT
1 TATATTAAATTA-AAAATAT-TTT
1550073 TATTATT-AATCTAAAAATATTTT
1 TA-TATTAAAT-TAAAAATATTTT
1550096 ATTTTTATTT
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
22 1 0.03
23 19 0.47
24 14 0.35
25 6 0.15
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (22 bp):
TATATTAAATTAAAAATATTTT
Found at i:1550098 original size:27 final size:25
Alignment explanation
Indices: 1550065--1550133 Score: 75
Period size: 27 Copynumber: 2.6 Consensus size: 25
1550055 AAATTATTAA
1550065 ATATATTTTATTATTAATCTAAAAAT
1 ATATATTTTATT-TTAATCTAAAAAT
* * *
1550091 ATTTTATTTTTATTTTCATTTAAAAAT
1 A-TATA-TTTTATTTTAATCTAAAAAT
*
1550118 ATATATTTTATGTTAA
1 ATATATTTTATTTTAA
1550134 AATTTATTTA
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
25 9 0.26
26 4 0.11
27 15 0.43
28 7 0.20
ACGTcount: A:0.39, C:0.03, G:0.01, T:0.57
Consensus pattern (25 bp):
ATATATTTTATTTTAATCTAAAAAT
Found at i:1550295 original size:31 final size:31
Alignment explanation
Indices: 1550252--1550324 Score: 110
Period size: 31 Copynumber: 2.4 Consensus size: 31
1550242 ACCCGTGATG
*
1550252 ATCACATCTTAATTAAATAAAAACGAAAATA
1 ATCATATCTTAATTAAATAAAAACGAAAATA
* * *
1550283 ATCATATCTTAATTAAATAAAAATGAAAGTG
1 ATCATATCTTAATTAAATAAAAACGAAAATA
1550314 ATCATATCTTA
1 ATCATATCTTA
1550325 TATTTTTTTG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.52, C:0.11, G:0.05, T:0.32
Consensus pattern (31 bp):
ATCATATCTTAATTAAATAAAAACGAAAATA
Found at i:1561827 original size:59 final size:59
Alignment explanation
Indices: 1561701--1561854 Score: 166
Period size: 59 Copynumber: 2.6 Consensus size: 59
1561691 TTGAGGGTTG
* * * * *
1561701 TTTTGTTGAATTTTTCAATTATTAAAAATTAAAAATATTTTTTAAATTATAAGATATTG
1 TTTTGTTGAGTTTTTTAATTATTAAAAATTAAAAATAATTTCTAAATTATAAGATATTA
* * ** * *
1561760 TCTCGTTGAGTTTTTTAATTATTAAAAATTAAAAATAATTTCTCGATTATAAGGTGTTA
1 TTTTGTTGAGTTTTTTAATTATTAAAAATTAAAAATAATTTCTAAATTATAAGATATTA
* * *
1561819 TTTTGTTGAGTTATTT-ATCTATTAAAAGTTACAAAT
1 TTTTGTTGAGTTTTTTAAT-TATTAAAAATTAAAAAT
1561855 GGTCAACAAC
Statistics
Matches: 78, Mismatches: 16, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
58 2 0.03
59 76 0.97
ACGTcount: A:0.37, C:0.05, G:0.10, T:0.49
Consensus pattern (59 bp):
TTTTGTTGAGTTTTTTAATTATTAAAAATTAAAAATAATTTCTAAATTATAAGATATTA
Found at i:1566920 original size:16 final size:15
Alignment explanation
Indices: 1566899--1566933 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
1566889 TAGGTGTGGT
1566899 TTTAAAAAAAATAAA
1 TTTAAAAAAAATAAA
1566914 GTTT-AAAAAAATAAA
1 -TTTAAAAAAAATAAA
1566929 TTTAA
1 TTTAA
1566934 GTAATAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
14 3 0.17
15 12 0.67
16 3 0.17
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (15 bp):
TTTAAAAAAAATAAA
Found at i:1569151 original size:2 final size:2
Alignment explanation
Indices: 1569144--1569202 Score: 93
Period size: 2 Copynumber: 30.0 Consensus size: 2
1569134 TAAAGGATGA
1569144 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
* *
1569186 AT A- AG AT AT TT AT AT AT
1 AT AT AT AT AT AT AT AT AT
1569203 TTTAATCGTG
Statistics
Matches: 53, Mismatches: 3, Indels: 2
0.91 0.05 0.03
Matches are distributed among these distances:
1 1 0.02
2 52 0.98
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1571037 original size:153 final size:153
Alignment explanation
Indices: 1570757--1571061 Score: 495
Period size: 153 Copynumber: 2.0 Consensus size: 153
1570747 TTACGTTGAT
* * * *
1570757 AATTAAATTAGGAAGGGGTTCTGATTGGTACACTGAAGAAATAGACTTTGCGGATCAATTGGTTG
1 AATTAAACTAGAAAGAGGTTCTGATTGGTACACTGAAGAAATAGACTGTGCGGATCAATTGGTTG
1570822 ATCATTGACGTCCTGTGACCATACTACGTGAATCATAAAAATATTATCATATGATTGCGGGAGAG
66 ATCATTGACGTCCTGTGACCATACTACGTGAATCATAAAAATATTATCATATGATTGCGGGAGAG
1570887 GATTTAGACAAACCCCATTTTTC
131 GATTTAGACAAACCCCATTTTTC
*
1570910 AATTAAACTAGAAAGAGGTTTTGATTGGTACACTG-AGTAAATAGACTGTGCGGATCAATTGGTT
1 AATTAAACTAGAAAGAGGTTCTGATTGGTACACTGAAG-AAATAGACTGTGCGGATCAATTGGTT
* * *
1570974 GATCATTGACGTCCTGTGACCATACTCCGTGAATCATAAAAATATTATCATATGGTTGTGGGAGA
65 GATCATTGACGTCCTGTGACCATACTACGTGAATCATAAAAATATTATCATATGATTGCGGGAGA
* * *
1571039 GGATTTAGATAAATCTCATTTTT
130 GGATTTAGACAAACCCCATTTTT
1571062 AGAATTACAA
Statistics
Matches: 140, Mismatches: 11, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
152 2 0.01
153 138 0.99
ACGTcount: A:0.32, C:0.14, G:0.22, T:0.32
Consensus pattern (153 bp):
AATTAAACTAGAAAGAGGTTCTGATTGGTACACTGAAGAAATAGACTGTGCGGATCAATTGGTTG
ATCATTGACGTCCTGTGACCATACTACGTGAATCATAAAAATATTATCATATGATTGCGGGAGAG
GATTTAGACAAACCCCATTTTTC
Found at i:1571969 original size:18 final size:19
Alignment explanation
Indices: 1571948--1571988 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
1571938 AATATTATAA
1571948 ATAAAT-AGA-ATAAAAAAT
1 ATAAATAAGATAT-AAAAAT
*
1571966 ATAATTAAGATATAAAAAT
1 ATAAATAAGATATAAAAAT
1571985 ATAA
1 ATAA
1571989 TTATATAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
18 5 0.25
19 13 0.65
20 2 0.10
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.27
Consensus pattern (19 bp):
ATAAATAAGATATAAAAAT
Found at i:1572220 original size:2 final size:2
Alignment explanation
Indices: 1572178--1572203 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1572168 AACTAAATTA
1572178 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
1572204 TTAAATAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1585500 original size:33 final size:33
Alignment explanation
Indices: 1585461--1585527 Score: 109
Period size: 33 Copynumber: 2.0 Consensus size: 33
1585451 ATCCGAACGG
*
1585461 GCTATGCGAGGGCATCCGAGGGCAA-CCGAGCGA
1 GCTATGCGAGGGAATCCGAGGG-AAGCCGAGCGA
1585494 GCTATGCGAGGGAATCCGAGGGAAGCCGAGCGA
1 GCTATGCGAGGGAATCCGAGGGAAGCCGAGCGA
1585527 G
1 G
1585528 GGTAGGTCGC
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 2 0.06
33 30 0.94
ACGTcount: A:0.25, C:0.24, G:0.42, T:0.09
Consensus pattern (33 bp):
GCTATGCGAGGGAATCCGAGGGAAGCCGAGCGA
Found at i:1585561 original size:18 final size:18
Alignment explanation
Indices: 1585538--1585572 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
1585528 GGTAGGTCGC
1585538 CCGGAGGGCATGGCGACT
1 CCGGAGGGCATGGCGACT
1585556 CCGGAGGGCATGGCGAC
1 CCGGAGGGCATGGCGAC
1585573 CTATGTGTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.29, G:0.46, T:0.09
Consensus pattern (18 bp):
CCGGAGGGCATGGCGACT
Found at i:1589049 original size:18 final size:18
Alignment explanation
Indices: 1589026--1589061 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1589016 TTTGATAGTC
1589026 GTAATTAATTTTTATAAT
1 GTAATTAATTTTTATAAT
* *
1589044 GTAATTCATTTTTCTAAT
1 GTAATTAATTTTTATAAT
1589062 TCTTTTGTAT
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:0.33, C:0.06, G:0.06, T:0.56
Consensus pattern (18 bp):
GTAATTAATTTTTATAAT
Done.