Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009591.1 Hibiscus syriacus cultivar Beakdansim tig00116970_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: 2451160
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 11
Found at i:1214506 original size:42 final size:41
Alignment explanation
Indices: 1214371--1214521 Score: 207
Period size: 42 Copynumber: 3.6 Consensus size: 41
1214361 CCAGTCGTTG
*
1214371 CGAATTTGGAATAAATCGCAACGCAAACTTCGACTATCGCAA
1 CGAATTTGG-ATAAATCGCAACGCGAACTTCGACTATCGCAA
1214413 CGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAA
1 CGAATTTGG-ATAAATCGCAACGCGAACTTCGACTATCGCAA
*
1214455 CGAATTTGGA-AACTCGCAACGCGAACTTCGACTATCGCAATA
1 CGAATTTGGATAAATCGCAACGCGAACTTCGACTATCGC-A-A
* * *
1214497 CGAACTTGGAT-TATCGCAATGCGAA
1 CGAATTTGGATAAATCGCAACGCGAA
1214522 TTATCGATCG
Statistics
Matches: 100, Mismatches: 6, Indels: 6
0.89 0.05 0.05
Matches are distributed among these distances:
40 27 0.27
41 2 0.02
42 71 0.71
ACGTcount: A:0.35, C:0.24, G:0.19, T:0.22
Consensus pattern (41 bp):
CGAATTTGGATAAATCGCAACGCGAACTTCGACTATCGCAA
Found at i:1217475 original size:23 final size:23
Alignment explanation
Indices: 1217449--1217499 Score: 102
Period size: 23 Copynumber: 2.2 Consensus size: 23
1217439 GGGAAGTGTT
1217449 ACAGAGAATATCAGTTACAGTTA
1 ACAGAGAATATCAGTTACAGTTA
1217472 ACAGAGAATATCAGTTACAGTTA
1 ACAGAGAATATCAGTTACAGTTA
1217495 ACAGA
1 ACAGA
1217500 AATGGGTTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.45, C:0.14, G:0.18, T:0.24
Consensus pattern (23 bp):
ACAGAGAATATCAGTTACAGTTA
Found at i:1223965 original size:21 final size:19
Alignment explanation
Indices: 1223941--1223993 Score: 72
Period size: 21 Copynumber: 2.7 Consensus size: 19
1223931 TCCCCTGTGG
1223941 GGGGAATCGATTCCCTTCAAA
1 GGGGAATCGATTCCC-TC-AA
*
1223962 GGGGAATCGGTTCCCTCAA
1 GGGGAATCGATTCCCTCAA
1223981 GGGG-ATCGATTCC
1 GGGGAATCGATTCC
1223994 TCTGCACCAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
18 8 0.27
19 6 0.20
20 2 0.07
21 14 0.47
ACGTcount: A:0.23, C:0.25, G:0.30, T:0.23
Consensus pattern (19 bp):
GGGGAATCGATTCCCTCAA
Found at i:1227189 original size:151 final size:150
Alignment explanation
Indices: 1226966--1227260 Score: 549
Period size: 151 Copynumber: 2.0 Consensus size: 150
1226956 ATCATGTATG
1226966 TATATATCCCTATTTTGACCAACAAGCATAATCGAAAATAGATGCATCAAATTATTTTTCAAAAG
1 TATATATCCCTATTTTGACCAACAAGCATAATCGAAAATAGATGCATCAAATTATTTTTCAAAAG
1227031 ATTATGGTTTTAACCCATTCACATATAAACATTATGCAATGTTGATTATAGAGATTAAGAGAACA
66 ATTATGGTTTTAACCCATTCACATATAAACATTATGCAATGTTGATTATAGAGATTAAGAGAACA
1227096 TGCATAAAGTTTTTTATGTA
131 TGCATAAAGTTTTTTATGTA
1227116 TATATATCCCTATTTTATGACCAACAAGCATAATCG-AAATAGATGCATCAAATT-TATTTTCAA
1 TATATATCCCTA-TTT-TGACCAACAAGCATAATCGAAAATAGATGCATCAAATTAT-TTTTCAA
1227179 AAGATTATGGTTTTAACCCATTCACATATAAACATTATGCAATGTTGATTATAGAGATTAAGAGA
63 AAGATTATGGTTTTAACCCATTCACATATAAACATTATGCAATGTTGATTATAGAGATTAAGAGA
1227244 ACATGCATAAAGTTTTT
128 ACATGCATAAAGTTTTT
1227261 GAAAATGTTA
Statistics
Matches: 142, Mismatches: 0, Indels: 5
0.97 0.00 0.03
Matches are distributed among these distances:
150 13 0.09
151 110 0.77
152 19 0.13
ACGTcount: A:0.39, C:0.14, G:0.12, T:0.35
Consensus pattern (150 bp):
TATATATCCCTATTTTGACCAACAAGCATAATCGAAAATAGATGCATCAAATTATTTTTCAAAAG
ATTATGGTTTTAACCCATTCACATATAAACATTATGCAATGTTGATTATAGAGATTAAGAGAACA
TGCATAAAGTTTTTTATGTA
Found at i:1228892 original size:22 final size:22
Alignment explanation
Indices: 1228864--1228908 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
1228854 AGCTACGTCC
1228864 ACTACCTTAGCTATCCACACTA
1 ACTACCTTAGCTATCCACACTA
1228886 ACTACCTTAGCTATCCACACTA
1 ACTACCTTAGCTATCCACACTA
1228908 A
1 A
1228909 GGATTTTCCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.33, C:0.36, G:0.04, T:0.27
Consensus pattern (22 bp):
ACTACCTTAGCTATCCACACTA
Found at i:1232048 original size:2 final size:2
Alignment explanation
Indices: 1232041--1232069 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1232031 AACTTCAACA
1232041 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
1232070 TCATAAAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:1233976 original size:30 final size:30
Alignment explanation
Indices: 1233940--1233998 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
1233930 TTTAATCCCT
* *
1233940 AAACTTT-TCAAAGTTTATACTTTGATCACC
1 AAACTTTACCAAA-TTTATAATTTGATCACC
*
1233970 AAACTTTACCAAATTTATAATTTGGTCAC
1 AAACTTTACCAAATTTATAATTTGATCAC
1233999 TAAATAAATC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.36, C:0.19, G:0.07, T:0.39
Consensus pattern (30 bp):
AAACTTTACCAAATTTATAATTTGATCACC
Found at i:1236430 original size:20 final size:20
Alignment explanation
Indices: 1236401--1236455 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 20
1236391 GAGGGTTCAT
* *
1236401 AGGTCTTTCGGGATATACAG
1 AGGTCATTCGGGACATACAG
*
1236421 AGGTCATTCGGGACATACAT
1 AGGTCATTCGGGACATACAG
* *
1236441 AGGCCATTCAGGACA
1 AGGTCATTCGGGACA
1236456 AATTTCATAT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.29, C:0.20, G:0.27, T:0.24
Consensus pattern (20 bp):
AGGTCATTCGGGACATACAG
Found at i:1240847 original size:23 final size:24
Alignment explanation
Indices: 1240792--1240848 Score: 64
Period size: 26 Copynumber: 2.4 Consensus size: 24
1240782 ATATTATTTT
1240792 ATTTAAA-AAATTAAAAAAAATAG
1 ATTTAAATAAATTAAAAAAAATAG
**
1240815 ATATTAAAATAAATTAAAATTAATA-
1 AT-TT-AAATAAATTAAAAAAAATAG
1240840 ATTTAAATA
1 ATTTAAATA
1240849 CTAAACCTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
23 7 0.24
24 4 0.14
25 5 0.17
26 13 0.45
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (24 bp):
ATTTAAATAAATTAAAAAAAATAG
Found at i:1248653 original size:19 final size:19
Alignment explanation
Indices: 1248629--1248698 Score: 131
Period size: 19 Copynumber: 3.7 Consensus size: 19
1248619 ATAGGATTTA
*
1248629 TGCATCGATGCATAAGGAG
1 TGCATCGATGCATAAAGAG
1248648 TGCATCGATGCATAAAGAG
1 TGCATCGATGCATAAAGAG
1248667 TGCATCGATGCATAAAGAG
1 TGCATCGATGCATAAAGAG
1248686 TGCATCGATGCAT
1 TGCATCGATGCAT
1248699 CCCCATTAAA
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
19 50 1.00
ACGTcount: A:0.33, C:0.17, G:0.27, T:0.23
Consensus pattern (19 bp):
TGCATCGATGCATAAAGAG
Found at i:1249400 original size:101 final size:102
Alignment explanation
Indices: 1249223--1249435 Score: 383
Period size: 101 Copynumber: 2.1 Consensus size: 102
1249213 GTAGAGGGTC
*
1249223 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACA-ATATGTATTCTTTGGAACATATGTGAGGTCTGGTGAGACACATAC
1249288 TTGATCCTTGGCATATGCATATGATTCTTAAGGAATGA
65 TTGATCCTTGGCATATGCATATGATTCTTAAGGAATGA
*
1249326 TATGTTGTCCTTCGGGAC-ATATGTATTCTTTGGAACATATGTGAGGTCTGGTGAGACACATACT
1 TATGTGGTCCTTCGGGACAATATGTATTCTTTGGAACATATGTGAGGTCTGGTGAGACACATACT
*
1249390 TGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TGATCCTTGGCATATGCATATGATTCTTAAGGAATGA
1249427 TATGTGGTC
1 TATGTGGTC
1249436 TTTATGGACA
Statistics
Matches: 106, Mismatches: 4, Indels: 2
0.95 0.04 0.02
Matches are distributed among these distances:
101 89 0.84
103 17 0.16
ACGTcount: A:0.25, C:0.14, G:0.25, T:0.36
Consensus pattern (102 bp):
TATGTGGTCCTTCGGGACAATATGTATTCTTTGGAACATATGTGAGGTCTGGTGAGACACATACT
TGATCCTTGGCATATGCATATGATTCTTAAGGAATGA
Found at i:1249490 original size:23 final size:23
Alignment explanation
Indices: 1249455--1249498 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
1249445 ATTATTATAT
*
1249455 GGCACTACGGTGCAATTCTACGC
1 GGCACTACAGTGCAATTCTACGC
*
1249478 GGCACTCCAGTGCAATTCTAC
1 GGCACTACAGTGCAATTCTAC
1249499 TGGCACTTAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.23, C:0.32, G:0.23, T:0.23
Consensus pattern (23 bp):
GGCACTACAGTGCAATTCTACGC
Found at i:1249512 original size:22 final size:23
Alignment explanation
Indices: 1249454--1249516 Score: 69
Period size: 23 Copynumber: 2.8 Consensus size: 23
1249444 CATTATTATA
1249454 TGGCAC-TACGGTGCAATTCTACG
1 TGGCACTTA-GGTGCAATTCTACG
* *
1249477 CGGCACTCCA-GTGCAATTCTAC-
1 TGGCACT-TAGGTGCAATTCTACG
1249499 TGGCACTTAGGTGCAATT
1 TGGCACTTAGGTGCAATT
1249517 ATATGAGCTG
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
21 1 0.03
22 14 0.42
23 17 0.52
25 1 0.03
ACGTcount: A:0.22, C:0.27, G:0.24, T:0.27
Consensus pattern (23 bp):
TGGCACTTAGGTGCAATTCTACG
Found at i:1255689 original size:64 final size:67
Alignment explanation
Indices: 1255621--1255748 Score: 201
Period size: 64 Copynumber: 2.0 Consensus size: 67
1255611 TTTAAAAAGA
1255621 AAACATCGAATAGGATTTATGCATCGATGCATAAG-G-AGTGCATCGATGCAT-CC-CCATTAAA
1 AAACATCGAATAGGATTTATGCATCGATGCAT-AGTGTAGTGCATCGATGCATACCTCCATTAAA
1255682 TAC
65 TAC
* *
1255685 AAACATCGAATAGGATTTATGCATCTATGCATGGTGTAGTGCATCGATGCATACCTCCATTAAA
1 AAACATCGAATAGGATTTATGCATCGATGCATAGTGTAGTGCATCGATGCATACCTCCATTAAA
1255749 AGATGAAAAT
Statistics
Matches: 58, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
63 1 0.02
64 32 0.55
65 15 0.26
66 2 0.03
67 8 0.14
ACGTcount: A:0.34, C:0.20, G:0.19, T:0.27
Consensus pattern (67 bp):
AAACATCGAATAGGATTTATGCATCGATGCATAGTGTAGTGCATCGATGCATACCTCCATTAAAT
AC
Found at i:1256376 original size:103 final size:103
Alignment explanation
Indices: 1256197--1256401 Score: 392
Period size: 103 Copynumber: 2.0 Consensus size: 103
1256187 GTAGAGGGTC
1256197 TATGTGGTCATTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
1 TATGTGGTCATTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
1256262 TTGATCCTTGGCATATGCATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGCATATGATTCTTAAGGAATGA
*
1256300 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
1 TATGTGGTCATTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
*
1256365 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATG
66 TTGATCCTTGGCATATGCATATGATTCTTAAGGAATG
1256402 TGTTGAGTTA
Statistics
Matches: 100, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
103 100 1.00
ACGTcount: A:0.25, C:0.14, G:0.25, T:0.36
Consensus pattern (103 bp):
TATGTGGTCATTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
TTGATCCTTGGCATATGCATATGATTCTTAAGGAATGA
Found at i:1257225 original size:75 final size:76
Alignment explanation
Indices: 1257098--1257304 Score: 271
Period size: 75 Copynumber: 2.8 Consensus size: 76
1257088 CCGTTGTACA
* * * *
1257098 AGGGGGGAATC-GTACCCCCT-TGGGGGGGATCGGTTCCCTCCGAGCATACTGGAATTCTCGGAG
1 AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAATTCTCGG-G
**
1257161 -CAAAACTGTTT
65 CCAAAACCATTT
*
1257172 AGGGGGGAATCGGTTCCTCCTAT-GGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGGC
1 AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAATTCTCGGGC
1257236 CAAAACCATTT
66 CAAAACCATTT
* * *
1257247 A-GGGGGAATCGGTTCCTCCTATGGGGGGGAATCGGTTCCCTCTGAGCAATCTGTAATT
1 AGGGGGGAATCGGTTCCTCCTAT-GGGGGGAATCGGTTCCCTCCGAGCATTCTGGAATT
1257305 TTTGGCTTTG
Statistics
Matches: 117, Mismatches: 11, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
74 33 0.28
75 53 0.45
76 31 0.26
ACGTcount: A:0.20, C:0.24, G:0.31, T:0.25
Consensus pattern (76 bp):
AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAATTCTCGGGC
CAAAACCATTT
Found at i:1265822 original size:74 final size:74
Alignment explanation
Indices: 1265652--1265855 Score: 266
Period size: 75 Copynumber: 2.7 Consensus size: 74
1265642 GACCGTTGAA
* * * * * *
1265652 CAGGGGGAATCGGTACCCCCT-TGGGGGGGATCGGTTCCCTCCGAGCATACTGGAATTCTCGGAA
1 CAGGGGGAATCGGTTCCTCCTAT-GGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCCCGGAA
**
1265716 CAAAACTGTT
65 CAAAACCATT
* *
1265726 TAGGGGGGAATCGGTTCCTCCTATGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCCCGGAG
1 CA-GGGGGAATCGGTTCCTCCTATGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCCCGGAA
*
1265791 CCAAACCATT
65 CAAAACCATT
* *
1265801 CAGGGGGAATCGGTTCCTCCTATGGGGGAATCGGTTCCCTCTGAGCAATCTGGAA
1 CAGGGGGAATCGGTTCCTCCTATGGGGGAATCGGTTCCCTCCGAGCATTCTGGAA
1265856 TTTTTGGCTT
Statistics
Matches: 114, Mismatches: 14, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
74 52 0.46
75 61 0.54
76 1 0.01
ACGTcount: A:0.21, C:0.25, G:0.31, T:0.23
Consensus pattern (74 bp):
CAGGGGGAATCGGTTCCTCCTATGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCCCGGAAC
AAAACCATT
Found at i:1266460 original size:88 final size:89
Alignment explanation
Indices: 1266332--1266542 Score: 275
Period size: 88 Copynumber: 2.4 Consensus size: 89
1266322 GGCCCAGGGC
* * * *
1266332 ATATCCTTAGGTTGATTCCCTTTTGCTGTGTGCTTAGGTAAC-CTTACGGATCTAAGGATATCCT
1 ATATCCTTAGATTGATTCCCTTATGCTGTGTGCCTAGGTAACTC-TACGGATCTAAGGATATCAT
1266396 TGGGTAGACCCATAGACCCCAAGGT
65 TGGGTAGACCCATAGACCCCAAGGT
* *
1266421 ATATCCTTAGATTGGTTCCCTTATG-T-TGTGCCTAGGGTAACTCTACGGATCTAATGATATCAT
1 ATATCCTTAGATTGATTCCCTTATGCTGTGTGCCTA-GGTAACTCTACGGATCTAAGGATATCAT
* * *
1266484 TGGGTAGGCCCATAGGCTCCAAGGT
65 TGGGTAGACCCATAGACCCCAAGGT
* *
1266509 ATATCCTTAGGTTGACTTCCCTTTTGCTGTGTGC
1 ATATCCTTAGATTGA-TTCCCTTATGCTGTGTGC
1266543 TGAGGGTAAG
Statistics
Matches: 105, Mismatches: 12, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
87 7 0.07
88 60 0.57
89 32 0.30
90 1 0.01
91 5 0.05
ACGTcount: A:0.21, C:0.22, G:0.23, T:0.35
Consensus pattern (89 bp):
ATATCCTTAGATTGATTCCCTTATGCTGTGTGCCTAGGTAACTCTACGGATCTAAGGATATCATT
GGGTAGACCCATAGACCCCAAGGT
Found at i:1271312 original size:18 final size:19
Alignment explanation
Indices: 1271275--1271312 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
1271265 ATAAAATGCA
1271275 TTTACAAATAAATAATATT
1 TTTACAAATAAATAATATT
*
1271294 TTTACAAATATAT-ATATT
1 TTTACAAATAAATAATATT
1271312 T
1 T
1271313 CTTATCGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (19 bp):
TTTACAAATAAATAATATT
Found at i:1273210 original size:10 final size:10
Alignment explanation
Indices: 1273195--1273242 Score: 51
Period size: 10 Copynumber: 4.7 Consensus size: 10
1273185 TATAAATTAA
1273195 AAATATAAAT
1 AAATATAAAT
1273205 AAATATAAAT
1 AAATATAAAT
* *
1273215 AAAAATATAT
1 AAATATAAAT
* *
1273225 AATTATAATAA
1 AAATATAA-AT
1273236 AAATATA
1 AAATATA
1273243 TTTTATGATA
Statistics
Matches: 30, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
10 23 0.77
11 7 0.23
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (10 bp):
AAATATAAAT
Found at i:1273236 original size:19 final size:20
Alignment explanation
Indices: 1273185--1273243 Score: 75
Period size: 19 Copynumber: 2.9 Consensus size: 20
1273175 AAAATTATTT
1273185 TATAAATTAAAAATATAAATAAA
1 TATAAA-TAAAAATAT--ATAAA
*
1273208 TATAAATAAAAATATATAAT
1 TATAAATAAAAATATATAAA
1273228 TAT-AATAAAAATATAT
1 TATAAATAAAAATATAT
1273244 TTTATGATAA
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
19 13 0.37
20 7 0.20
22 9 0.26
23 6 0.17
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (20 bp):
TATAAATAAAAATATATAAA
Found at i:1273346 original size:20 final size:21
Alignment explanation
Indices: 1273295--1273347 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 21
1273285 GAATTTTATT
1273295 TATTTTTAAGTAATTAAAATA
1 TATTTTTAAGTAATTAAAATA
* * **
1273316 AATTATTAAGTAA-TAAGTTA
1 TATTTTTAAGTAATTAAAATA
1273336 TATTTTTAAGTA
1 TATTTTTAAGTA
1273348 TGTTAGTATT
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
20 15 0.58
21 11 0.42
ACGTcount: A:0.45, C:0.00, G:0.08, T:0.47
Consensus pattern (21 bp):
TATTTTTAAGTAATTAAAATA
Found at i:1278666 original size:15 final size:14
Alignment explanation
Indices: 1278646--1278680 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
1278636 TAATTATATG
1278646 TTTAATATTTTATAA
1 TTTAATATTTT-TAA
1278661 TTTAATATTTTTAA
1 TTTAATATTTTTAA
*
1278675 ATTAAT
1 TTTAAT
1278681 TTAATGGTGC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.42
15 11 0.58
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (14 bp):
TTTAATATTTTTAA
Found at i:1282217 original size:32 final size:31
Alignment explanation
Indices: 1282145--1282220 Score: 93
Period size: 31 Copynumber: 2.5 Consensus size: 31
1282135 AGGACTGTGA
*
1282145 CCCC-CCAAAATTTTAAAAATTTTAATTTTG
1 CCCCTCCAAAATTTTAAAAAATTTAATTTTG
* * *
1282175 ACACT-TAAAATTCTTAAAAAATTTAATTTTG
1 CCCCTCCAAAATT-TTAAAAAATTTAATTTTG
1282206 CCCCTCCAAAATTTT
1 CCCCTCCAAAATTTT
1282221 TAGGAATTCA
Statistics
Matches: 36, Mismatches: 7, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
30 8 0.22
31 22 0.61
32 6 0.17
ACGTcount: A:0.38, C:0.20, G:0.03, T:0.39
Consensus pattern (31 bp):
CCCCTCCAAAATTTTAAAAAATTTAATTTTG
Found at i:1292748 original size:20 final size:21
Alignment explanation
Indices: 1292714--1292756 Score: 79
Period size: 20 Copynumber: 2.1 Consensus size: 21
1292704 CTGGAGGTTC
1292714 ATTACTCTAAATAGTATCGTT
1 ATTACTCTAAATAGTATCGTT
1292735 ATTACTCT-AATAGTATCGTT
1 ATTACTCTAAATAGTATCGTT
1292755 AT
1 AT
1292757 ATTGTGCTAG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 14 0.64
21 8 0.36
ACGTcount: A:0.33, C:0.14, G:0.09, T:0.44
Consensus pattern (21 bp):
ATTACTCTAAATAGTATCGTT
Found at i:1296576 original size:53 final size:53
Alignment explanation
Indices: 1296362--1296788 Score: 432
Period size: 53 Copynumber: 7.9 Consensus size: 53
1296352 CATTTGCCAC
* *
1296362 CTAACTTGCATTAGTGACACCTTTCTGCCAAAATGCACCA-TTAGGCATTAACTTTTCAT
1 CTAACTTGCATTATTGACACCTTTCTGCCAATATGCA-CAGTTAGGC-----C-TTTCAT
* * * * *
1296421 CTAACTTGCATTAGTGGCACCTTTCTGCCAA-ATGAACAATTAGGACTTTCAT
1 CTAACTTGCATTATTGACACCTTTCTGCCAATATGCACAGTTAGGCCTTTCAT
* *
1296473 CTAACTTGCATTATTGGCACCTTTCTGCCAA-ATGCACA-TCTATGCCTTTCAT
1 CTAACTTGCATTATTGACACCTTTCTGCCAATATGCACAGT-TAGGCCTTTCAT
* * * * *
1296525 GTAACTTGCATTATTGACATCTTTATGTCAATATGCACAGTTAGGCCTTTCAA
1 CTAACTTGCATTATTGACACCTTTCTGCCAATATGCACAGTTAGGCCTTTCAT
*
1296578 CTAACTTGCATTATTGACACCTTTCTGCCAATATGCATAGTTAGGCATTTAACATTTCAT
1 CTAACTTGCATTATTGACACCTTTCTGCCAATATGCACAGTTAGGC------C-TTTCAT
* * * *
1296638 CTAACTTGAATTATTGTCACATTTATGCCAA-ATGCACAGTTAGGCCTTTCAT
1 CTAACTTGCATTATTGACACCTTTCTGCCAATATGCACAGTTAGGCCTTTCAT
* * ** * *
1296690 CTAACTTGTATTATTGATATATTTATGACAATATGCACAGTTAGGCCTTTCAT
1 CTAACTTGCATTATTGACACCTTTCTGCCAATATGCACAGTTAGGCCTTTCAT
* * *
1296743 CTAATTTGCATTATTGACACCTTTCTTCCAATATGCATAGTTAGGC
1 CTAACTTGCATTATTGACACCTTTCTGCCAATATGCACAGTTAGGC
1296789 ATTTAACTTT
Statistics
Matches: 317, Mismatches: 39, Indels: 30
0.82 0.10 0.08
Matches are distributed among these distances:
51 1 0.00
52 110 0.35
53 118 0.37
54 1 0.00
57 2 0.01
58 9 0.03
59 44 0.14
60 32 0.10
ACGTcount: A:0.28, C:0.22, G:0.13, T:0.37
Consensus pattern (53 bp):
CTAACTTGCATTATTGACACCTTTCTGCCAATATGCACAGTTAGGCCTTTCAT
Found at i:1296673 original size:165 final size:165
Alignment explanation
Indices: 1296467--1296800 Score: 526
Period size: 165 Copynumber: 2.0 Consensus size: 165
1296457 CAATTAGGAC
* * * * *
1296467 TTTCATCTAACTTGCATTATTGGCACCTTTCTGCCAAATGCACA-TCTATGCCTTTCATGTAACT
1 TTTCATCTAACTTGAATTATTGGCACATTTATGCCAAATGCACAGT-TAGGCCTTTCATCTAACT
* *
1296531 TGCATTATTGACATCTTTATGTCAATATGCACAGTTAGGCCTTTCAACTAACTTGCATTATTGAC
65 TGCATTATTGACATATTTATGACAATATGCACAGTTAGGCCTTTCAACTAACTTGCATTATTGAC
1296596 ACCTTTCTGCCAATATGCATAGTTAGGCATTTAACA
130 ACCTTTCTGCCAATATGCATAGTTAGGCATTTAACA
*
1296632 TTTCATCTAACTTGAATTATTGTCACATTTATGCCAAATGCACAGTTAGGCCTTTCATCTAACTT
1 TTTCATCTAACTTGAATTATTGGCACATTTATGCCAAATGCACAGTTAGGCCTTTCATCTAACTT
* * * *
1296697 GTATTATTGATATATTTATGACAATATGCACAGTTAGGCCTTTCATCTAATTTGCATTATTGACA
66 GCATTATTGACATATTTATGACAATATGCACAGTTAGGCCTTTCAACTAACTTGCATTATTGACA
* *
1296762 CCTTTCTTCCAATATGCATAGTTAGGCATTTAACT
131 CCTTTCTGCCAATATGCATAGTTAGGCATTTAACA
1296797 TTTC
1 TTTC
1296801 TTCATTCATT
Statistics
Matches: 154, Mismatches: 14, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
165 153 0.99
166 1 0.01
ACGTcount: A:0.27, C:0.21, G:0.12, T:0.40
Consensus pattern (165 bp):
TTTCATCTAACTTGAATTATTGGCACATTTATGCCAAATGCACAGTTAGGCCTTTCATCTAACTT
GCATTATTGACATATTTATGACAATATGCACAGTTAGGCCTTTCAACTAACTTGCATTATTGACA
CCTTTCTGCCAATATGCATAGTTAGGCATTTAACA
Found at i:1296703 original size:112 final size:113
Alignment explanation
Indices: 1296519--1296796 Score: 306
Period size: 112 Copynumber: 2.5 Consensus size: 113
1296509 CATCTATGCC
* * *
1296519 TTTCATGTAACTTGCATTATTGACATCTTTATGTCAATATGCACAGTTAGGCCTTTCAACTAACT
1 TTTCATCTAACTTGAATTATTGACATCTTTATGCCAATATGCACAGTTAGGCCTTTCAACTAACT
* * * *
1296584 TGCATTATTGACACCTTTCTGCCAATATGCATAGTTAGGCATTTAACA
66 TGCATTATTGACACATTTATGACAATATGCACAGTTAGGCATTTAACA
* *
1296632 TTTCATCTAACTTGAATTATTGTCA-CATTTATGCCAA-ATGCACAGTTAGGCCTTTCATCTAAC
1 TTTCATCTAACTTGAATTATTGACATC-TTTATGCCAATATGCACAGTTAGGCCTTTCAACTAAC
* * *
1296695 TTGTATTATTGATATATTTATGACAATATGCACAGTTAGGC------C-
65 TTGCATTATTGACACATTTATGACAATATGCACAGTTAGGCATTTAACA
* * * * * * *
1296737 TTTCATCTAATTTGCATTATTGACACCTTTCTTCCAATATGCATAGTTAGGCATTT-AACT
1 TTTCATCTAACTTGAATTATTGACATCTTTATGCCAATATGCACAGTTAGGCCTTTCAACT
1296797 TTTCTTCATT
Statistics
Matches: 142, Mismatches: 20, Indels: 14
0.81 0.11 0.08
Matches are distributed among these distances:
105 33 0.23
106 18 0.13
112 60 0.42
113 31 0.22
ACGTcount: A:0.28, C:0.19, G:0.13, T:0.40
Consensus pattern (113 bp):
TTTCATCTAACTTGAATTATTGACATCTTTATGCCAATATGCACAGTTAGGCCTTTCAACTAACT
TGCATTATTGACACATTTATGACAATATGCACAGTTAGGCATTTAACA
Found at i:1300608 original size:20 final size:20
Alignment explanation
Indices: 1300583--1300637 Score: 92
Period size: 20 Copynumber: 2.8 Consensus size: 20
1300573 TTTACACTTA
1300583 GGGAACCGATTCCCCATGAG
1 GGGAACCGATTCCCCATGAG
1300603 GGGAACCGATTCCCCATGAG
1 GGGAACCGATTCCCCATGAG
* *
1300623 GGGTATCGATTCCCC
1 GGGAACCGATTCCCC
1300638 CCACGCTCTA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.22, C:0.31, G:0.29, T:0.18
Consensus pattern (20 bp):
GGGAACCGATTCCCCATGAG
Found at i:1306328 original size:22 final size:22
Alignment explanation
Indices: 1306302--1306382 Score: 78
Period size: 23 Copynumber: 3.7 Consensus size: 22
1306292 ATAGGGCAGA
*
1306302 GGGAATCGATACCCCCTTGAAG
1 GGGAACCGATACCCCCTTGAAG
*
1306324 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATACCCCC-TTGAAG
*
1306347 GGGAGCCGACT-CCCCCTT--AG
1 GGGAACCGA-TACCCCCTTGAAG
* *
1306367 GGGAATCAATACCCCC
1 GGGAACCGATACCCCC
1306383 CTGGGTTCTG
Statistics
Matches: 50, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
19 1 0.02
20 13 0.26
22 16 0.32
23 19 0.38
24 1 0.02
ACGTcount: A:0.23, C:0.33, G:0.26, T:0.17
Consensus pattern (22 bp):
GGGAACCGATACCCCCTTGAAG
Found at i:1306344 original size:23 final size:23
Alignment explanation
Indices: 1306302--1306364 Score: 83
Period size: 23 Copynumber: 2.8 Consensus size: 23
1306292 ATAGGGCAGA
* *
1306302 GGGAATCGATACCCCC-TTGAAG
1 GGGAACCGATTCCCCCTTTGAAG
1306324 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATTCCCCCTTTGAAG
* *
1306347 GGGAGCCGACTCCCCCTT
1 GGGAACCGATTCCCCCTT
1306365 AGGGGAATCA
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
22 14 0.39
23 22 0.61
ACGTcount: A:0.21, C:0.33, G:0.27, T:0.19
Consensus pattern (23 bp):
GGGAACCGATTCCCCCTTTGAAG
Found at i:1311404 original size:46 final size:46
Alignment explanation
Indices: 1311348--1311435 Score: 124
Period size: 46 Copynumber: 1.9 Consensus size: 46
1311338 TAATACATCG
* * *
1311348 TTATGTATTTTGATTTATGGCATCCTTTCATG-TCGATAATGCACCA
1 TTATGAATTTTCATTTATGGCATCATTTCATGCT-GATAATGCACCA
*
1311394 TTATGAATTTTCATTTATGGCCTCATTTCATGCTGATAATGC
1 TTATGAATTTTCATTTATGGCATCATTTCATGCTGATAATGC
1311436 GTCATTTGTC
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
46 36 0.97
47 1 0.03
ACGTcount: A:0.24, C:0.17, G:0.15, T:0.44
Consensus pattern (46 bp):
TTATGAATTTTCATTTATGGCATCATTTCATGCTGATAATGCACCA
Found at i:1311619 original size:53 final size:53
Alignment explanation
Indices: 1311502--1312259 Score: 898
Period size: 53 Copynumber: 14.0 Consensus size: 53
1311492 GCATTTAACT
* * * *
1311502 TTTCATCTAACTTGCATTAGTGGA-ACCTTTCTTCCAA-ATGCACAATTAGTCC
1 TTTCATCTAACTTGCATTA-TTGACACCTTTCTGCCAATATGCACAGTTAGGCC
* * *
1311554 TTTCATCTAACTTGCATTATTGCCACTTTTCTGCCAATATGCACAGCTAGGCC
1 TTTCATCTAACTTGCATTATTGACACCTTTCTGCCAATATGCACAGTTAGGCC
* * * *
1311607 TTTCATCTAACTTGCATTATTGACACATTTCTTCCAATATGCATAGTTAAGCATTTAAC
1 TTTCATCTAACTTGCATTATTGACACCTTTCTGCCAATATGCACAGTTAGGC------C
* * *
1311666 ATTTCATCTAACTTGCATTATTGGCACATTTCTGCCAA-ATGCACAGTTAGGTC
1 -TTTCATCTAACTTGCATTATTGACACCTTTCTGCCAATATGCACAGTTAGGCC
* ** * *
1311719 TTTCATCTAAGTTGCATTATTGACATATTTCTTCCAATATGCACAATTAGGCC
1 TTTCATCTAACTTGCATTATTGACACCTTTCTGCCAATATGCACAGTTAGGCC
* *
1311772 TTTCATCTAACTTGCATTATTGACACCTTTCTGTCAATATGCATAGTTAGGCATTTAAC
1 TTTCATCTAACTTGCATTATTGACACCTTTCTGCCAATATGCACAGTTAGGC------C
* * *
1311831 ATTTCATCTAACTTGCATTATTGGCTCCTTTATGCCAA-ATGCACAGTTAGGCC
1 -TTTCATCTAACTTGCATTATTGACACCTTTCTGCCAATATGCACAGTTAGGCC
* * *
1311884 TTTCATCTAACTTGTATTATTGACACCTTTCTGTCAATATGCATAGTTAGGCC
1 TTTCATCTAACTTGCATTATTGACACCTTTCTGCCAATATGCACAGTTAGGCC
* * * *
1311937 TTTCATCTAACTTACATTATTGACACCTTTTTGTCAATATGCACAGTTAGACC
1 TTTCATCTAACTTGCATTATTGACACCTTTCTGCCAATATGCACAGTTAGGCC
* *
1311990 TTTCATCTAACTTGCATTATTGACACCTTTCTGCCACTGTGCACAGTTAGGCATTTAAC
1 TTTCATCTAACTTGCATTATTGACACCTTTCTGCCAATATGCACAGTTAGGC------C
1312049 ATTTCATCTAACTTGCATTATT-AGCACCTTTCTGCCAA-ATGCACAGTTAGGCC
1 -TTTCATCTAACTTGCATTATTGA-CACCTTTCTGCCAATATGCACAGTTAGGCC
* *
1312102 TTTTATCTAACTTGCATTATTGACACCTTTCTGCCAATATGCACTGTTAGGCC
1 TTTCATCTAACTTGCATTATTGACACCTTTCTGCCAATATGCACAGTTAGGCC
* * * *
1312155 TTTCATCTAACTTGTATTATTGACACATTTATGCCAATATGCAGAGTTAGGCC
1 TTTCATCTAACTTGCATTATTGACACCTTTCTGCCAATATGCACAGTTAGGCC
* *
1312208 TTTCATCTAACTTGCATTATTGACACCTTTTTGCAAATATGCACAGTTAGGC
1 TTTCATCTAACTTGCATTATTGACACCTTTCTGCCAATATGCACAGTTAGGC
1312260 ATTTAACTTT
Statistics
Matches: 610, Mismatches: 68, Indels: 55
0.83 0.09 0.08
Matches are distributed among these distances:
51 2 0.00
52 129 0.21
53 336 0.55
59 41 0.07
60 102 0.17
ACGTcount: A:0.26, C:0.23, G:0.13, T:0.38
Consensus pattern (53 bp):
TTTCATCTAACTTGCATTATTGACACCTTTCTGCCAATATGCACAGTTAGGCC
Found at i:1311724 original size:165 final size:165
Alignment explanation
Indices: 1311444--1312259 Score: 913
Period size: 165 Copynumber: 5.0 Consensus size: 165
1311434 GCGTCATTTG
* * * * * * * * *
1311444 TCATATAACTTGCATTAGTGTCACATTTCTACTAAAATGCACCA-TTAGGCATTTAACTTTTCAT
1 TCATCTAACTTGCATTATTGACACCTTTCTTCCAATATGCA-TAGTTAGGCATTTAACATTTCAT
* * * *
1311508 CTAACTTGCATTAGTGGAACCTTTCTTCCAAATGCACAATTA-GTCCTTTCATCTAACTTGCATT
65 CTAACTTGCATTATTGGCACCTTTCTGCCAAATGCACAGTTAGGT-CTTTCATCTAACTTGCATT
* *
1311572 ATTGCCACTTTTCTGCCAATATGCACAGCTAGGCCTT
129 ATTGACACTTTTCTGCCAATATGCACAGTTAGGCCTT
* *
1311609 TCATCTAACTTGCATTATTGACACATTTCTTCCAATATGCATAGTTAAGCATTTAACATTTCATC
1 TCATCTAACTTGCATTATTGACACCTTTCTTCCAATATGCATAGTTAGGCATTTAACATTTCATC
* *
1311674 TAACTTGCATTATTGGCACATTTCTGCCAAATGCACAGTTAGGTCTTTCATCTAAGTTGCATTAT
66 TAACTTGCATTATTGGCACCTTTCTGCCAAATGCACAGTTAGGTCTTTCATCTAACTTGCATTAT
* *
1311739 TGACA-TATTTCTTCCAATATGCACAATTAGGCCTT
131 TGACACT-TTTCTGCCAATATGCACAGTTAGGCCTT
1311774 TCATCTAACTTGCATTATTGACACCTTTCTGT-CAATATGCATAGTTAGGCATTTAACATTTCAT
1 TCATCTAACTTGCATTATTGACACCTTTCT-TCCAATATGCATAGTTAGGCATTTAACATTTCAT
* * * *
1311838 CTAACTTGCATTATTGGCTCCTTTATGCCAAATGCACAGTTAGGCCTTTCATCTAACTTGTATTA
65 CTAACTTGCATTATTGGCACCTTTCTGCCAAATGCACAGTTAGGTCTTTCATCTAACTTGCATTA
* * *
1311903 TTGACACCTTTCTGTCAATATGCATAGTTAGGCCTT
130 TTGACACTTTTCTGCCAATATGCACAGTTAGGCCTT
* * * *
1311939 TCATCTAACTTACATTATTGACACCTTT-TTGTCAATATGCACAGTTA-G------ACCTTTCAT
1 TCATCTAACTTGCATTATTGACACCTTTCTT-CCAATATGCATAGTTAGGCATTTAACATTTCAT
* **
1311996 CTAACTTGCATTATTGACACCTTTCTGCCACTGTGCACAGTTAGGCATTTAACATTTCATCTAAC
65 CTAACTTGCATTATTGGCACCTTTCTGCCA-AATGCACAGTTAGG----T--C-TTTCATCTAAC
*
1312061 TTGCATTATT-AGCACCTTTCTGCCAA-ATGCACAGTTAGGCCTT
122 TTGCATTATTGA-CACTTTTCTGCCAATATGCACAGTTAGGCCTT
* *
1312104 TTATCTAACTTGCATTATTGACACCTTTCTGCCAATATGCACT-GTTAGGC------C-TTTCAT
1 TCATCTAACTTGCATTATTGACACCTTTCTTCCAATATGCA-TAGTTAGGCATTTAACATTTCAT
* * * * * *
1312161 CTAACTTGTATTATTGACACATTTATGCCAATATGCAGAGTTAGGCCTTTCATCTAACTTGCATT
65 CTAACTTGCATTATTGGCACCTTTCTGCCAA-ATGCACAGTTAGGTCTTTCATCTAACTTGCATT
*
1312226 ATTGACACCTTTT-TGCAAATATGCACAGTTAGGC
129 ATTGACA-CTTTTCTGCCAATATGCACAGTTAGGC
1312260 ATTTAACTTT
Statistics
Matches: 569, Mismatches: 58, Indels: 54
0.84 0.09 0.08
Matches are distributed among these distances:
158 63 0.11
159 32 0.06
163 1 0.00
164 4 0.01
165 430 0.76
166 39 0.07
ACGTcount: A:0.27, C:0.23, G:0.12, T:0.38
Consensus pattern (165 bp):
TCATCTAACTTGCATTATTGACACCTTTCTTCCAATATGCATAGTTAGGCATTTAACATTTCATC
TAACTTGCATTATTGGCACCTTTCTGCCAAATGCACAGTTAGGTCTTTCATCTAACTTGCATTAT
TGACACTTTTCTGCCAATATGCACAGTTAGGCCTT
Found at i:1311801 original size:27 final size:26
Alignment explanation
Indices: 1311718--1311802 Score: 64
Period size: 27 Copynumber: 3.2 Consensus size: 26
1311708 ACAGTTAGGT
*
1311718 CTTTCATCTAAGTTGCATTATTGACAT
1 CTTTCATCTAA-TTGCATTATTGACAC
* * * ** **
1311745 ATTTCTTCCAATATGCACAATT-AGGC
1 CTTTCATCTAAT-TGCATTATTGACAC
1311771 CTTTCATCTAACTTGCATTATTGACAC
1 CTTTCATCTAA-TTGCATTATTGACAC
1311798 CTTTC
1 CTTTC
1311803 TGTCAATATG
Statistics
Matches: 40, Mismatches: 15, Indels: 6
0.66 0.25 0.10
Matches are distributed among these distances:
26 17 0.43
27 23 0.57
ACGTcount: A:0.26, C:0.24, G:0.09, T:0.41
Consensus pattern (26 bp):
CTTTCATCTAATTGCATTATTGACAC
Found at i:1311934 original size:218 final size:218
Alignment explanation
Indices: 1311502--1312271 Score: 997
Period size: 218 Copynumber: 3.5 Consensus size: 218
1311492 GCATTTAACT
* * *
1311502 TTTCATCTAACTTGCATTAGTGGA-ACCTTTCTTCCAA-ATGCACAATTAGTCCTTTCATCTAAC
1 TTTCATCTAACTTGCATTA-TTGACACATTTCTTCCAATATGCACAATTAGGCCTTTCATCTAAC
* * *
1311565 TTGCATTATTGCCACTTTTCTGCCAATATGCACAGCTAGGC------C-TTTCATCTAACTTGCA
65 TTGCATTATTGACACCTTTCTGCCAATATGCACAGTTAGGCATTTAACATTTCATCTAACTTGCA
* * * * *
1311623 TTATTGACACATTTCTTCCAATATGCATAGTTAAGCATTTAACATTTCATCTAACTTGCATTATT
130 TTATTGGCACCTTTCTGCCAA-ATGCACAGTTAGGC------C-TTTCATCTAACTTGCATTATT
* * * *
1311688 GGCACATTTCTGCCAA-ATGCACAGTTAGGTC
187 GACACCTTTCTGCCAATATGCATAGTTAGGCC
* *
1311719 TTTCATCTAAGTTGCATTATTGACATATTTCTTCCAATATGCACAATTAGGCCTTTCATCTAACT
1 TTTCATCTAACTTGCATTATTGACACATTTCTTCCAATATGCACAATTAGGCCTTTCATCTAACT
* *
1311784 TGCATTATTGACACCTTTCTGTCAATATGCATAGTTAGGCATTTAACATTTCATCTAACTTGCAT
66 TGCATTATTGACACCTTTCTGCCAATATGCACAGTTAGGCATTTAACATTTCATCTAACTTGCAT
* * *
1311849 TATTGGCTCCTTTATGCCAAATGCACAGTTAGGCCTTTCATCTAACTTGTATTATTGACACCTTT
131 TATTGGCACCTTTCTGCCAAATGCACAGTTAGGCCTTTCATCTAACTTGCATTATTGACACCTTT
*
1311914 CTGTCAATATGCATAGTTAGGCC
196 CTGCCAATATGCATAGTTAGGCC
* * * * *
1311937 TTTCATCTAACTTACATTATTGACACCTTT-TTGTCAATATGCACAGTTAGACCTTTCATCTAAC
1 TTTCATCTAACTTGCATTATTGACACATTTCTT-CCAATATGCACAATTAGGCCTTTCATCTAAC
* *
1312001 TTGCATTATTGACACCTTTCTGCCACTGTGCACAGTTAGGCATTTAACATTTCATCTAACTTGCA
65 TTGCATTATTGACACCTTTCTGCCAATATGCACAGTTAGGCATTTAACATTTCATCTAACTTGCA
* *
1312066 TTATTAGCACCTTTCTGCCAAATGCACAGTTAGGCCTTTTATCTAACTTGCATTATTGACACCTT
130 TTATTGGCACCTTTCTGCCAAATGCACAGTTAGGCCTTTCATCTAACTTGCATTATTGACACCTT
1312131 TCTGCCAATATGCACT-GTTAGGCC
195 TCTGCCAATATGCA-TAGTTAGGCC
* * * * *
1312155 TTTCATCTAACTTGTATTATTGACACATTTATGCCAATATGCAGAGTTAGGCCTTTCATCTAACT
1 TTTCATCTAACTTGCATTATTGACACATTTCTTCCAATATGCACAATTAGGCCTTTCATCTAACT
* * *
1312220 TGCATTATTGACACCTTTTTGCAAATATGCACAGTTAGGCATTTAACTTTTC
66 TGCATTATTGACACCTTTCTGCCAATATGCACAGTTAGGCATTTAACATTTC
1312272 TTCATTCATT
Statistics
Matches: 488, Mismatches: 52, Indels: 25
0.86 0.09 0.04
Matches are distributed among these distances:
216 3 0.01
217 64 0.13
218 374 0.77
219 2 0.00
224 13 0.03
225 32 0.07
ACGTcount: A:0.26, C:0.23, G:0.12, T:0.38
Consensus pattern (218 bp):
TTTCATCTAACTTGCATTATTGACACATTTCTTCCAATATGCACAATTAGGCCTTTCATCTAACT
TGCATTATTGACACCTTTCTGCCAATATGCACAGTTAGGCATTTAACATTTCATCTAACTTGCAT
TATTGGCACCTTTCTGCCAAATGCACAGTTAGGCCTTTCATCTAACTTGCATTATTGACACCTTT
CTGCCAATATGCATAGTTAGGCC
Found at i:1312018 original size:27 final size:27
Alignment explanation
Indices: 1311882--1312020 Score: 87
Period size: 27 Copynumber: 5.2 Consensus size: 27
1311872 CACAGTTAGG
*
1311882 CCTTTCATCTAACTTGTATTATTGACA
1 CCTTTCATCTAACTTGCATTATTGACA
* **
1311909 CCTTTC-TGTCAA-TATGCA-TAGTT-AGG
1 CCTTTCATCT-AACT-TGCATTA-TTGACA
*
1311935 CCTTTCATCTAACTTACATTATTGACA
1 CCTTTCATCTAACTTGCATTATTGACA
* * * *
1311962 CCTTT-TTGTCAA-TATGCA-CAGTT-AGA
1 CCTTTCATCT-AACT-TGCATTA-TTGACA
1311988 CCTTTCATCTAACTTGCATTATTGACA
1 CCTTTCATCTAACTTGCATTATTGACA
1312015 CCTTTC
1 CCTTTC
1312021 TGCCACTGTG
Statistics
Matches: 81, Mismatches: 17, Indels: 28
0.64 0.13 0.22
Matches are distributed among these distances:
26 38 0.47
27 43 0.53
ACGTcount: A:0.25, C:0.24, G:0.10, T:0.41
Consensus pattern (27 bp):
CCTTTCATCTAACTTGCATTATTGACA
Found at i:1312236 original size:27 final size:27
Alignment explanation
Indices: 1312100--1312237 Score: 74
Period size: 27 Copynumber: 5.2 Consensus size: 27
1312090 CACAGTTAGG
*
1312100 CCTTTTATCTAACTTGCATTATTGACA
1 CCTTTCATCTAACTTGCATTATTGACA
* * * **
1312127 CCTTTC-TGCCAA-TATGCACTGTT-AGG
1 CCTTTCAT-CTAACT-TGCATTATTGACA
*
1312153 CCTTTCATCTAACTTGTATTATTGACA
1 CCTTTCATCTAACTTGCATTATTGACA
* * * **
1312180 CATTT-ATGCCAA-TATGCA-GAGTT-AGG
1 CCTTTCAT-CTAACT-TGCATTA-TTGACA
1312206 CCTTTCATCTAACTTGCATTATTGACA
1 CCTTTCATCTAACTTGCATTATTGACA
1312233 CCTTT
1 CCTTT
1312238 TTGCAAATAT
Statistics
Matches: 76, Mismatches: 23, Indels: 24
0.62 0.19 0.20
Matches are distributed among these distances:
26 36 0.47
27 40 0.53
ACGTcount: A:0.25, C:0.23, G:0.12, T:0.40
Consensus pattern (27 bp):
CCTTTCATCTAACTTGCATTATTGACA
Found at i:1312670 original size:21 final size:21
Alignment explanation
Indices: 1312644--1312685 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
1312634 TTTCTATTAC
1312644 AAGTTCAGCCTATCTTACAAT
1 AAGTTCAGCCTATCTTACAAT
*
1312665 AAGTTCATCCTATCTTACAAT
1 AAGTTCAGCCTATCTTACAAT
1312686 TACTGACTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.33, C:0.24, G:0.07, T:0.36
Consensus pattern (21 bp):
AAGTTCAGCCTATCTTACAAT
Found at i:1313819 original size:85 final size:85
Alignment explanation
Indices: 1313654--1314163 Score: 440
Period size: 85 Copynumber: 6.0 Consensus size: 85
1313644 TCCGTAAATA
* * ** * * * * * *
1313654 GTTGATATGCTTATTTCTCTAAAGTATATCAAATC-GAAGAATGATCTTGCACTTTTATATGAAT
1 GTTGATATGCTTCTTTCTCTAAAGGATGCCAAATCAG-AGAACGATCTTGCTCCTTTCTCTGAAG
* * * *
1313718 AACACCAATTCA-TAATCAATA
65 GACGCCAAGT-AGTAATCAATG
* * * * * * * * *
1313739 GTTTATTTG-TTCTTATCTCTAAAGAACGCTAAATCAAAGAACTATCTTGCTCCTTTATCTGAAT
1 GTTGATATGCTTCTT-TCTCTAAAGGATGCCAAATCAGAGAACGATCTTGCTCCTTTCTCTGAAG
* *
1313803 GATGCCAAGTCGTAATCAATG
65 GACGCCAAGTAGTAATCAATG
* * * * * *
1313824 GTTGATATGCTCCTTTCTCTAAAGGATGCCAAACCGGATAACGATCCTT-CTCCATTCTATGAAG
1 GTTGATATGCTTCTTTCTCTAAAGGATGCCAAATCAGAGAACGAT-CTTGCTCCTTTCTCTGAAG
* *
1313888 GACACCAAGTAGTAACCAATG
65 GACGCCAAGTAGTAATCAATG
* * * * * * * **
1313909 GTTGATCTGCTCCTTTCTCTGAAGGATGCCAAATCAGGGAACGATCTTGCTCATTTATCTAAAAA
1 GTTGATATGCTTCTTTCTCTAAAGGATGCCAAATCAGAGAACGATCTTGCTCCTTTCTCTGAAGG
1313974 ACGCCAAGTAGTAATCAATG
66 ACGCCAAGTAGTAATCAATG
*
1313994 GTTGATATG-TTCCTTTCTCTAAAGGATGCCAAATCAGAGAACAATCTTGCTCCTTTCTCTGAAG
1 GTTGATATGCTT-CTTTCTCTAAAGGATGCCAAATCAGAGAACGATCTTGCTCCTTTCTCTGAAG
* *
1314058 GACACCAAGTTGTAATCAATG
65 GACGCCAAGTAGTAATCAATG
* * * * * *
1314079 GTTTATCTGCTTCTTTCTCTGAAGGATGTCAAATCA-AGGAATGATCTTACTCCTTTCTCTGAAG
1 GTTGATATGCTTCTTTCTCTAAAGGATGCCAAATCAGA-GAACGATCTTGCTCCTTTCTCTGAAG
*
1314143 GATGCCAAGTCA-TAATCAATG
65 GACGCCAAGT-AGTAATCAATG
1314164 AAAATTCAAT
Statistics
Matches: 339, Mismatches: 76, Indels: 20
0.78 0.17 0.05
Matches are distributed among these distances:
84 9 0.03
85 321 0.95
86 9 0.03
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.33
Consensus pattern (85 bp):
GTTGATATGCTTCTTTCTCTAAAGGATGCCAAATCAGAGAACGATCTTGCTCCTTTCTCTGAAGG
ACGCCAAGTAGTAATCAATG
Found at i:1313958 original size:170 final size:170
Alignment explanation
Indices: 1313769--1314163 Score: 540
Period size: 170 Copynumber: 2.3 Consensus size: 170
1313759 AAAGAACGCT
* * *
1313769 AAATCAAAGAACTATCTTGCTCCTTTATCTGAATGATGCCAAGTCGTAATCAATGGTTGATATGC
1 AAATCAAGGAACGATCTTGCTCCTTTATCTGAAAGATGCCAAGTCGTAATCAATGGTTGATATGC
* * *
1313834 TCCTTTCTCTAAAGGATGCCAAACCGGATAACGATCCTT-CTCCATTCTATGAAGGACACCAAGT
66 TCCTTTCTCTAAAGGATGCCAAACCAGAGAACAAT-CTTGCTCCATTCTATGAAGGACACCAAGT
1313898 AGTAACCAATGGTTGATCTGCTCCTTTCTCTGAAGGATGCC
130 AGTAACCAATGGTTGATCTGCTCCTTTCTCTGAAGGATGCC
* * * * * * *
1313939 AAATCAGGGAACGATCTTGCTCATTTATCTAAAAAACGCCAAGTAGTAATCAATGGTTGATATGT
1 AAATCAAGGAACGATCTTGCTCCTTTATCTGAAAGATGCCAAGTCGTAATCAATGGTTGATATGC
* * * *
1314004 TCCTTTCTCTAAAGGATGCCAAATCAGAGAACAATCTTGCTCCTTTCTCTGAAGGACACCAAGTT
66 TCCTTTCTCTAAAGGATGCCAAACCAGAGAACAATCTTGCTCCATTCTATGAAGGACACCAAGTA
* * * *
1314069 GTAATCAATGGTTTATCTGCTTCTTTCTCTGAAGGATGTC
131 GTAACCAATGGTTGATCTGCTCCTTTCTCTGAAGGATGCC
* * * * *
1314109 AAATCAAGGAATGATCTTACTCCTTTCTCTGAAGGATGCCAAGTCATAATCAATG
1 AAATCAAGGAACGATCTTGCTCCTTTATCTGAAAGATGCCAAGTCGTAATCAATG
1314164 AAAATTCAAT
Statistics
Matches: 192, Mismatches: 32, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
169 3 0.02
170 189 0.98
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.31
Consensus pattern (170 bp):
AAATCAAGGAACGATCTTGCTCCTTTATCTGAAAGATGCCAAGTCGTAATCAATGGTTGATATGC
TCCTTTCTCTAAAGGATGCCAAACCAGAGAACAATCTTGCTCCATTCTATGAAGGACACCAAGTA
GTAACCAATGGTTGATCTGCTCCTTTCTCTGAAGGATGCC
Found at i:1315298 original size:76 final size:76
Alignment explanation
Indices: 1315172--1315321 Score: 300
Period size: 76 Copynumber: 2.0 Consensus size: 76
1315162 TGTGAAAAGT
1315172 CTTCTTGTGCTTGATCAAAAGATATTTTCATTTTTCTACCTCGCTTCTTCTTATTGCTTCAGCCT
1 CTTCTTGTGCTTGATCAAAAGATATTTTCATTTTTCTACCTCGCTTCTTCTTATTGCTTCAGCCT
1315237 CTTACTTTTGC
66 CTTACTTTTGC
1315248 CTTCTTGTGCTTGATCAAAAGATATTTTCATTTTTCTACCTCGCTTCTTCTTATTGCTTCAGCCT
1 CTTCTTGTGCTTGATCAAAAGATATTTTCATTTTTCTACCTCGCTTCTTCTTATTGCTTCAGCCT
1315313 CTTACTTTT
66 CTTACTTTT
1315322 TGCCCCACTT
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
76 74 1.00
ACGTcount: A:0.16, C:0.25, G:0.10, T:0.49
Consensus pattern (76 bp):
CTTCTTGTGCTTGATCAAAAGATATTTTCATTTTTCTACCTCGCTTCTTCTTATTGCTTCAGCCT
CTTACTTTTGC
Found at i:1320115 original size:28 final size:26
Alignment explanation
Indices: 1320058--1320116 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 26
1320048 AATGAAAGAA
**
1320058 TAAAAAATAAAGAAAAATAATTAATT
1 TAAAAAATAAAGAAAAATAATTAAAC
**
1320084 TAAAAAATAAAGAGAATTTAAATTAAAC
1 TAAAAAATAAAGA-AAAAT-AATTAAAC
1320112 TAAAA
1 TAAAA
1320117 TTTTAATAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 13 0.48
27 3 0.11
28 11 0.41
ACGTcount: A:0.68, C:0.02, G:0.05, T:0.25
Consensus pattern (26 bp):
TAAAAAATAAAGAAAAATAATTAAAC
Found at i:1320902 original size:15 final size:14
Alignment explanation
Indices: 1320876--1320922 Score: 67
Period size: 14 Copynumber: 3.3 Consensus size: 14
1320866 TATTGATTTT
*
1320876 TTTTAAATTTTAAA
1 TTTTAAAATTTAAA
1320890 TTTTAAAGATTTAAA
1 TTTTAAA-ATTTAAA
*
1320905 TTTTAAAATTTTAA
1 TTTTAAAATTTAAA
1320919 TTTT
1 TTTT
1320923 TTTGGGATTG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
14 17 0.57
15 13 0.43
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (14 bp):
TTTTAAAATTTAAA
Found at i:1320923 original size:7 final size:7
Alignment explanation
Indices: 1320876--1320922 Score: 60
Period size: 7 Copynumber: 6.6 Consensus size: 7
1320866 TATTGATTTT
1320876 TTTTAAA
1 TTTTAAA
1320883 TTTTAAA
1 TTTTAAA
1320890 TTTTAAA
1 TTTTAAA
*
1320897 GATTTAAA
1 -TTTTAAA
1320905 TTTTAAAA
1 TTTT-AAA
1320913 TTTT-AA
1 TTTTAAA
1320919 TTTT
1 TTTT
1320923 TTTGGGATTG
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
6 6 0.17
7 17 0.47
8 13 0.36
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (7 bp):
TTTTAAA
Found at i:1320923 original size:15 final size:15
Alignment explanation
Indices: 1320875--1320922 Score: 64
Period size: 15 Copynumber: 3.3 Consensus size: 15
1320865 ATATTGATTT
*
1320875 TTTTTAAATTTTAAA
1 TTTTAAAATTTTAAA
1320890 TTTTAAAGA-TTTAAA
1 TTTTAAA-ATTTTAAA
1320905 TTTTAAAATTTT-AA
1 TTTTAAAATTTTAAA
1320919 TTTT
1 TTTT
1320923 TTTGGGATTG
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
14 7 0.23
15 22 0.73
16 1 0.03
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (15 bp):
TTTTAAAATTTTAAA
Found at i:1321431 original size:12 final size:12
Alignment explanation
Indices: 1321397--1321442 Score: 65
Period size: 12 Copynumber: 3.8 Consensus size: 12
1321387 TTTATCCAGG
1321397 TTATTATTAATA
1 TTATTATTAATA
*
1321409 TTTATTTTTAATA
1 -TTATTATTAATA
1321422 TTATTATTAATA
1 TTATTATTAATA
*
1321434 TTAATATTA
1 TTATTATTA
1321443 CAGGTTTTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
12 19 0.63
13 11 0.37
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (12 bp):
TTATTATTAATA
Found at i:1324924 original size:4 final size:4
Alignment explanation
Indices: 1324915--1324940 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
1324905 TTCCTCAAAC
1324915 TTAT TTAT TTAT TTAT TTAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TT
1324941 GCAAAAAGCA
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:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTAT
Found at i:1326203 original size:21 final size:20
Alignment explanation
Indices: 1326174--1326212 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
1326164 TAAGGCATTA
*
1326174 AACATCATAAAGAAAACAAAC
1 AACAACATAAA-AAAACAAAC
*
1326195 AACAACATACAAAAACAA
1 AACAACATAAAAAAACAA
1326213 TCATCCATTA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.69, C:0.21, G:0.03, T:0.08
Consensus pattern (20 bp):
AACAACATAAAAAAACAAAC
Found at i:1326729 original size:25 final size:27
Alignment explanation
Indices: 1326677--1326729 Score: 65
Period size: 25 Copynumber: 2.0 Consensus size: 27
1326667 AAGAGGGTGA
*
1326677 GCAGTTGTGGCAGTTGTCCCCTCCTGG
1 GCAGTTGTGGCAGTGGTCCCCTCCTGG
* *
1326704 GCAGTTG-GGCA-TGGTCCTCTCTTGG
1 GCAGTTGTGGCAGTGGTCCCCTCCTGG
1326729 G
1 G
1326730 TAGCTTGTAG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 12 0.52
26 4 0.17
27 7 0.30
ACGTcount: A:0.08, C:0.26, G:0.36, T:0.30
Consensus pattern (27 bp):
GCAGTTGTGGCAGTGGTCCCCTCCTGG
Found at i:1331793 original size:14 final size:15
Alignment explanation
Indices: 1331766--1331890 Score: 66
Period size: 15 Copynumber: 8.6 Consensus size: 15
1331756 TAAGAACAAC
1331766 AAAAGAGAAAATAAA
1 AAAAGAGAAAATAAA
*
1331781 AAAAGAG-AGATAAA
1 AAAAGAGAAAATAAA
* * * **
1331795 AAAGGGGAAAAGATG
1 AAAAGAGAAAATAAA
1331810 AAAA-A-AAAA-AAA
1 AAAAGAGAAAATAAA
1331822 AAAA-AGAAAATAACA
1 AAAAGAGAAAATAA-A
*
1331837 AAAAGA-AAAAAAAA
1 AAAAGAGAAAATAAA
* * *
1331851 AGAAAAAAAAAAGAAA
1 A-AAAGAGAAAATAAA
* *
1331867 AAAA-AAAAGAAAAAA
1 AAAAGAGAA-AATAAA
1331882 AAAAGAGAA
1 AAAAGAGAA
1331891 CAAATCAAGT
Statistics
Matches: 85, Mismatches: 16, Indels: 17
0.72 0.14 0.14
Matches are distributed among these distances:
12 6 0.07
13 8 0.09
14 19 0.22
15 40 0.47
16 12 0.14
ACGTcount: A:0.82, C:0.01, G:0.14, T:0.03
Consensus pattern (15 bp):
AAAAGAGAAAATAAA
Found at i:1331814 original size:1 final size:1
Alignment explanation
Indices: 1331810--1331885 Score: 89
Period size: 1 Copynumber: 76.0 Consensus size: 1
1331800 GGAAAAGATG
* * * * * *
1331810 AAAAAAAAAAAAAAAAAGAAAATAACAAAAAGAAAAAAAAAAGAAAAAAAAAAGAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
*
1331875 GAAAAAAAAAA
1 AAAAAAAAAAA
1331886 GAGAACAAAT
Statistics
Matches: 61, Mismatches: 14, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
1 61 1.00
ACGTcount: A:0.91, C:0.01, G:0.07, T:0.01
Consensus pattern (1 bp):
A
Found at i:1331839 original size:22 final size:23
Alignment explanation
Indices: 1331811--1331885 Score: 114
Period size: 23 Copynumber: 3.2 Consensus size: 23
1331801 GAAAAGATGA
1331811 AAAAAAAAAAAAAAAAGAAAATAA
1 AAAAAAAAAAAAAAAAGAAAA-AA
*
1331835 CAAAAAGAAAAAAAAAAGAAAAAA
1 -AAAAAAAAAAAAAAAAGAAAAAA
*
1331859 AAAAGAAAAAAAAAAAGAAAAAA
1 AAAAAAAAAAAAAAAAGAAAAAA
1331882 AAAA
1 AAAA
1331886 GAGAACAAAT
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
23 25 0.53
24 2 0.04
25 20 0.43
ACGTcount: A:0.91, C:0.01, G:0.07, T:0.01
Consensus pattern (23 bp):
AAAAAAAAAAAAAAAAGAAAAAA
Found at i:1331886 original size:11 final size:11
Alignment explanation
Indices: 1331810--1331887 Score: 113
Period size: 11 Copynumber: 6.8 Consensus size: 11
1331800 GGAAAAGATG
1331810 AAAAAAA-AAA
1 AAAAAAAGAAA
1331820 AAAAAAAGAAAA
1 AAAAAAAG-AAA
1331832 TAACAAAAAGAAA
1 -AA-AAAAAGAAA
1331845 AAAAAAAGAAA
1 AAAAAAAGAAA
1331856 AAAAAAAGAAAA
1 AAAAAAAG-AAA
1331868 AAAAAAAGAAA
1 AAAAAAAGAAA
1331879 AAAAAAAGA
1 AAAAAAAGA
1331888 GAACAAATCA
Statistics
Matches: 63, Mismatches: 0, Indels: 9
0.88 0.00 0.12
Matches are distributed among these distances:
10 7 0.11
11 29 0.46
12 16 0.25
13 5 0.08
14 6 0.10
ACGTcount: A:0.90, C:0.01, G:0.08, T:0.01
Consensus pattern (11 bp):
AAAAAAAGAAA
Found at i:1331886 original size:34 final size:36
Alignment explanation
Indices: 1331810--1331887 Score: 135
Period size: 34 Copynumber: 2.2 Consensus size: 36
1331800 GGAAAAGATG
1331810 AAAAAAA-AAAAAAAAAAGAAAATAACAAAAAGAAA
1 AAAAAAAGAAAAAAAAAAGAAAATAACAAAAAGAAA
1331845 AAAAAAAGAAAAAAAAAAGAAAA-AA-AAAAAGAAA
1 AAAAAAAGAAAAAAAAAAGAAAATAACAAAAAGAAA
1331879 AAAAAAAGA
1 AAAAAAAGA
1331888 GAACAAATCA
Statistics
Matches: 42, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
34 18 0.43
35 9 0.21
36 15 0.36
ACGTcount: A:0.90, C:0.01, G:0.08, T:0.01
Consensus pattern (36 bp):
AAAAAAAGAAAAAAAAAAGAAAATAACAAAAAGAAA
Found at i:1333020 original size:3 final size:3
Alignment explanation
Indices: 1333012--1333102 Score: 159
Period size: 3 Copynumber: 31.0 Consensus size: 3
1333002 TTTTATTCGG
1333012 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
1333059 TTA TTA TTA TTA TTA TTA TTA TTA -TA TTG TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1333103 CAGGTTTTTA
Statistics
Matches: 84, Mismatches: 2, Indels: 4
0.93 0.02 0.04
Matches are distributed among these distances:
2 4 0.05
3 80 0.95
ACGTcount: A:0.33, C:0.00, G:0.01, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:1333286 original size:28 final size:29
Alignment explanation
Indices: 1333226--1333286 Score: 97
Period size: 28 Copynumber: 2.1 Consensus size: 29
1333216 TCAACCATTG
* *
1333226 GATCTGCCTAGATCAGATCTAATGGTCAT
1 GATCTACCTAGATCAGATCCAATGGTCAT
1333255 GATCTACCTAGATCA-ATCCAATGGTCAT
1 GATCTACCTAGATCAGATCCAATGGTCAT
1333283 GATC
1 GATC
1333287 CTTGGATGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
28 16 0.53
29 14 0.47
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.30
Consensus pattern (29 bp):
GATCTACCTAGATCAGATCCAATGGTCAT
Found at i:1337817 original size:17 final size:18
Alignment explanation
Indices: 1337781--1337820 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
1337771 AAAAATTTAA
1337781 AAAATAAGTATGATAAAT
1 AAAATAAGTATGATAAAT
1337799 AAAATAAG-AT-ATAAAAT
1 AAAATAAGTATGAT-AAAT
1337816 AAAAT
1 AAAAT
1337821 TGAGTGAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 2 0.10
17 11 0.52
18 8 0.38
ACGTcount: A:0.68, C:0.00, G:0.07, T:0.25
Consensus pattern (18 bp):
AAAATAAGTATGATAAAT
Found at i:1341995 original size:22 final size:22
Alignment explanation
Indices: 1341949--1341999 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 22
1341939 CGTATAATTA
* * * *
1341949 TAAATTAGTTAAAATCATATGG
1 TAAATTATTTAAAATAAAATAG
1341971 TAAATTATTTAAAATAAAATAG
1 TAAATTATTTAAAATAAAATAG
1341993 T-AATTAT
1 TAAATTAT
1342000 ATTATTTTTC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
21 6 0.24
22 19 0.76
ACGTcount: A:0.51, C:0.02, G:0.08, T:0.39
Consensus pattern (22 bp):
TAAATTATTTAAAATAAAATAG
Found at i:1352598 original size:18 final size:18
Alignment explanation
Indices: 1352575--1352609 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
1352565 TAGTGCATGC
1352575 GACTTGTGTGGTGTTAGT
1 GACTTGTGTGGTGTTAGT
1352593 GACTTGTGTGGTGTTAG
1 GACTTGTGTGGTGTTAG
1352610 CGAAGATCAT
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:0.11, C:0.06, G:0.40, T:0.43
Consensus pattern (18 bp):
GACTTGTGTGGTGTTAGT
Found at i:1356595 original size:2 final size:2
Alignment explanation
Indices: 1356588--1356627 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1356578 TAACCTTATT
1356588 TA TA TA TA TA TA TA TA 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
1356628 GTTCAACTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1356835 original size:13 final size:15
Alignment explanation
Indices: 1356817--1356853 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
1356807 TAAATAAAAT
1356817 TATTAT-TAT-TATA
1 TATTATATATATATA
1356830 TATTATATATATATA
1 TATTATATATATATA
1356845 TA-TATATAT
1 TATTATATAT
1356854 GAGGTGATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 6 0.27
14 10 0.45
15 6 0.27
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
TATTATATATATATA
Found at i:1361990 original size:27 final size:26
Alignment explanation
Indices: 1361947--1361997 Score: 75
Period size: 27 Copynumber: 1.9 Consensus size: 26
1361937 TAATTATTAC
*
1361947 CTACCCACTAATCACCTATCCCACTA
1 CTACCCACTAATCACCTAACCCACTA
*
1361973 CTACCCACCTAATTACCTAACCCAC
1 CTACCCA-CTAATCACCTAACCCAC
1361998 CACCATCATC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.31, C:0.47, G:0.00, T:0.22
Consensus pattern (26 bp):
CTACCCACTAATCACCTAACCCACTA
Found at i:1362889 original size:22 final size:23
Alignment explanation
Indices: 1362861--1362909 Score: 73
Period size: 22 Copynumber: 2.2 Consensus size: 23
1362851 TTATTCATTT
*
1362861 TTTTTAATTTGAGCAT-TTTTTG
1 TTTTTAATTTGAGCATGTTTTTA
*
1362883 TTTTTAATTTTAGCATGTTTTTA
1 TTTTTAATTTGAGCATGTTTTTA
1362906 TTTT
1 TTTT
1362910 ATTTATTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 15 0.62
23 9 0.38
ACGTcount: A:0.18, C:0.04, G:0.10, T:0.67
Consensus pattern (23 bp):
TTTTTAATTTGAGCATGTTTTTA
Found at i:1362920 original size:15 final size:15
Alignment explanation
Indices: 1362900--1362957 Score: 61
Period size: 15 Copynumber: 4.0 Consensus size: 15
1362890 TTTTAGCATG
1362900 TTTTTATTTTATTTA
1 TTTTTATTTTATTTA
1362915 TTTTTATTTT-TTTA
1 TTTTTATTTTATTTA
*
1362929 CTTCTTA--TTATTT-
1 -TTTTTATTTTATTTA
1362942 TTTATTATTTTATTTA
1 TTT-TTATTTTATTTA
1362958 ACATTTATTA
Statistics
Matches: 35, Mismatches: 2, Indels: 11
0.73 0.04 0.23
Matches are distributed among these distances:
12 2 0.06
13 5 0.14
14 7 0.20
15 21 0.60
ACGTcount: A:0.19, C:0.03, G:0.00, T:0.78
Consensus pattern (15 bp):
TTTTTATTTTATTTA
Found at i:1362967 original size:29 final size:27
Alignment explanation
Indices: 1362908--1362972 Score: 78
Period size: 29 Copynumber: 2.3 Consensus size: 27
1362898 TGTTTTTATT
*
1362908 TTATTTATTTTTATTTTTTTACTTCTTA
1 TTATTT-TTTTTATTTTTTTACATCTTA
1362936 TTATTTTTTATTATTTTATTTAACAT-TTA
1 TTATTTTTT-TTATTTT-TTT-ACATCTTA
1362965 TTATTTTT
1 TTATTTTT
1362973 CCCTTTGATT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
27 3 0.09
28 13 0.39
29 14 0.42
30 3 0.09
ACGTcount: A:0.22, C:0.05, G:0.00, T:0.74
Consensus pattern (27 bp):
TTATTTTTTTTATTTTTTTACATCTTA
Found at i:1362993 original size:24 final size:24
Alignment explanation
Indices: 1362960--1363032 Score: 72
Period size: 24 Copynumber: 3.4 Consensus size: 24
1362950 TTTATTTAAC
*
1362960 ATTTATTATTTTTCCCTTTGATTT
1 ATTTAATATTTTTCCCTTTGATTT
1362984 ATTTAATA-TTTT---TTT-A-TT
1 ATTTAATATTTTTCCCTTTGATTT
1363002 -TTT-ATATTTTTCCCTTTGATTT
1 ATTTAATATTTTTCCCTTTGATTT
*
1363024 ATATAATAT
1 ATTTAATAT
1363033 CTATTTATTA
Statistics
Matches: 39, Mismatches: 2, Indels: 16
0.68 0.04 0.28
Matches are distributed among these distances:
16 3 0.08
17 7 0.18
18 2 0.05
19 1 0.03
20 6 0.15
21 1 0.03
22 2 0.05
23 6 0.15
24 11 0.28
ACGTcount: A:0.23, C:0.08, G:0.03, T:0.66
Consensus pattern (24 bp):
ATTTAATATTTTTCCCTTTGATTT
Found at i:1363011 original size:40 final size:44
Alignment explanation
Indices: 1362961--1363047 Score: 137
Period size: 40 Copynumber: 2.1 Consensus size: 44
1362951 TTATTTAACA
*
1362961 TTTATTATTTTTCCCTTTGATTTATTTAATAT-T-TTT-TTATT
1 TTTATTATTTTTCCCTTTGATTTATATAATATCTATTTATTATT
1363002 TTTA-TATTTTTCCCTTTGATTTATATAATATCTATTTATTATT
1 TTTATTATTTTTCCCTTTGATTTATATAATATCTATTTATTATT
1363045 TTT
1 TTT
1363048 TGACTTTTTA
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
40 26 0.62
41 5 0.12
42 3 0.07
43 8 0.19
ACGTcount: A:0.22, C:0.08, G:0.02, T:0.68
Consensus pattern (44 bp):
TTTATTATTTTTCCCTTTGATTTATATAATATCTATTTATTATT
Found at i:1368180 original size:83 final size:83
Alignment explanation
Indices: 1367930--1368748 Score: 960
Period size: 83 Copynumber: 9.7 Consensus size: 83
1367920 TACAGTATAA
* *
1367930 CTCAAGGTGAGAAGGGCTATCTGTCAACCAAAACCTTCGAGTTCGATTACATTCAGCTCAAGGGC
1 CTCAAGGCGAGAAGGGCTATCTATCAA-C-AAACCTTCGAGTTCGATTACATTCAGCTCAAGGGC
1367995 ATATCAAATTTGCAGCATAG
64 ATATCAAATTTGCAGCATAG
* * *
1368015 CTCAAGGTGAGAAGGGTTATCTGCCA-CAAACAAACCTTCGAGTTCGATTACATTCATCTCAAGG
1 CTCAAGGCGAGAAGGGCTATCT---ATC-AACAAACCTTCGAGTTCGATTACATTCAGCTCAAGG
**
1368079 GCATATCAAATTTATAGCATAG
62 GCATATCAAATTTGCAGCATAG
* * * *
1368101 CTCAAGGTGAGAAGGGATATCTATCAACAAACCTTCGAGTTCGATTCCATTCAGCTCAAGGGCGT
1 CTCAAGGCGAGAAGGGCTATCTATCAACAAACCTTCGAGTTCGATTACATTCAGCTCAAGGGCAT
* *
1368166 ATCAAATTTGTAGCAGAG
66 ATCAAATTTGCAGCATAG
* * * *
1368184 CTCAAGGCGAGAAGGGTTATCTGTCAACCAAAACCTTCGAGTTTGATTACATTCAGCTCAGGGGC
1 CTCAAGGCGAGAAGGGCTATCTATCAA-C-AAACCTTCGAGTTCGATTACATTCAGCTCAAGGGC
* * *
1368249 ATGTCAAATTTACAACATAG
64 ATATCAAATTTGCAGCATAG
* * *
1368269 CTCAAGGCGAGAAGGGCTATCTGTCAAAAAACCTTCGAGTTCGATTACATTCAACTCAAGGGCAT
1 CTCAAGGCGAGAAGGGCTATCTATCAACAAACCTTCGAGTTCGATTACATTCAGCTCAAGGGCAT
*
1368334 ATCAAATTGGCAGCATAG
66 ATCAAATTTGCAGCATAG
* * * * * **
1368352 CTCAAGACAAGAAGGGTTATCTACCAGCAACAAACCTTTGAGTTTAATTACATTCAGCTCAAGGG
1 CTCAAGGCGAGAAGGGCTATCT---ATCAACAAACCTTCGAGTTCGATTACATTCAGCTCAAGGG
* *
1368417 CATATCAAATTCGCAGTATAG
63 CATATCAAATTTGCAGCATAG
* * ** * * *
1368438 CTCAAGGCGAGAAGGGCTATCTATCAATAAAACTTCGAGTTTAATTCCATTCATCAT-AAGGGCG
1 CTCAAGGCGAGAAGGGCTATCTATCAACAAACCTTCGAGTTCGATTACATTCAGC-TCAAGGGCA
1368502 TATCAAATTTGCAGCATAG
65 TATCAAATTTGCAGCATAG
* * * * *
1368521 CTCAAGGCGAGAAGGGCTATATATCAACAAACCTTTGAGTTCAATTCCATTCAGCTCAAGGGCGT
1 CTCAAGGCGAGAAGGGCTATCTATCAACAAACCTTCGAGTTCGATTACATTCAGCTCAAGGGCAT
* *
1368586 ATCAAATTTGTATCATAG
66 ATCAAATTTGCAGCATAG
* *
1368604 CTCAAGGCGTGAAGGGCTATCTATCAACCAAAACCTTCGAGTTTGATTACATTCAGCTC-AGGGA
1 CTCAAGGCGAGAAGGGCTATCTATCAA-C-AAACCTTCGAGTTCGATTACATTCAGCTCAAGGG-
* *
1368668 CATGTCAAATTTTCAGCATAG
63 CATATCAAATTTGCAGCATAG
* * * *
1368689 CTCAAGGCGAGAAGGGCTATCTGTCAACAAAAAACTGTCAAGTTCGATTTCATTCAGCTC
1 CTCAAGGCGAGAAGGGCTATCTATCAAC--AAACCT-TCGAGTTCGATTACATTCAGCTC
1368749 GACGACACAT
Statistics
Matches: 636, Mismatches: 81, Indels: 33
0.85 0.11 0.04
Matches are distributed among these distances:
82 1 0.00
83 293 0.46
84 9 0.01
85 165 0.26
86 164 0.26
87 2 0.00
88 2 0.00
ACGTcount: A:0.33, C:0.21, G:0.20, T:0.26
Consensus pattern (83 bp):
CTCAAGGCGAGAAGGGCTATCTATCAACAAACCTTCGAGTTCGATTACATTCAGCTCAAGGGCAT
ATCAAATTTGCAGCATAG
Found at i:1368639 original size:337 final size:339
Alignment explanation
Indices: 1367930--1368710 Score: 1099
Period size: 337 Copynumber: 2.3 Consensus size: 339
1367920 TACAGTATAA
*
1367930 CTCAAGGTGAGAAGGGCTATCTGTCAACCAAAACCTTCGAGTTCGATTACATTCAGCTCAAGGGC
1 CTCAAGGCGAGAAGGGCTATCTGTCAACCAAAACCTTCGAGTTCGATTACATTCAGCTCAAGGGC
* *
1367995 ATATCAAATTTGCAGCATAGCTCAAGGTGAGAAGGGTTATCTGCCACAAACAAACCTTCGAGTTC
66 ATATCAAATTTGCAGCATAGCTCAAGGCGAGAAGGGTTATCTACCACAAACAAACCTTCGAGTTC
* * * * *
1368060 GATTACATTCATCTCAAGGGCATATCAAATTTATAGCATAGCTCAAGGTGAGAAGGGATATCTAT
131 AATTACATTCAGCTCAAGGGCATATCAAATTCACAGCATAGCTCAAGGCGAGAAGGGATATCTAT
* * *
1368125 CAACAAACCTTCGAGTTCGATTCCATTCAGCTCAAGGGCGTATCAAATTTGTAGCAGAGCTCAAG
196 CAACAAAACTTCGAGTTCAATTCCATTCAGCTCAAGGGCGTATCAAATTTGCAGCAGAGCTCAAG
* * * ** * *
1368190 GCGAGAAGGGTTATCTGTCAACCAAAACCTTCGAGTTTGATTACATTCAGCTCAGGGGCATGTCA
261 GCGAGAAGGGCTATATATCAACCAAAACCTTCGAGTTCAATTACATTCAGCTCAAGGGCATATCA
1368255 AATTTACAACATAG
326 AATTTACAACATAG
*
1368269 CTCAAGGCGAGAAGGGCTATCTGTCAA--AAAACCTTCGAGTTCGATTACATTCAACTCAAGGGC
1 CTCAAGGCGAGAAGGGCTATCTGTCAACCAAAACCTTCGAGTTCGATTACATTCAGCTCAAGGGC
* * * *
1368332 ATATCAAATTGGCAGCATAGCTCAAGACAAGAAGGGTTATCTACCAGC-AACAAACCTTTGAGTT
66 ATATCAAATTTGCAGCATAGCTCAAGGCGAGAAGGGTTATCTACCA-CAAACAAACCTTCGAGTT
* * * *
1368396 TAATTACATTCAGCTCAAGGGCATATCAAATTCGCAGTATAGCTCAAGGCGAGAAGGGCTATCTA
130 CAATTACATTCAGCTCAAGGGCATATCAAATTCACAGCATAGCTCAAGGCGAGAAGGGATATCTA
* * * *
1368461 TCAATAAAACTTCGAGTTTAATTCCATTCATCAT-AAGGGCGTATCAAATTTGCAGCATAGCTCA
195 TCAACAAAACTTCGAGTTCAATTCCATTCAGC-TCAAGGGCGTATCAAATTTGCAGCAGAGCTCA
* * *
1368525 AGGCGAGAAGGGCTATATATCAA-C-AAACCTTTGAGTTCAATTCCATTCAGCTCAAGGGCGTAT
259 AGGCGAGAAGGGCTATATATCAACCAAAACCTTCGAGTTCAATTACATTCAGCTCAAGGGCATAT
** *
1368588 CAAATTTGTATCATAG
324 CAAATTTACAACATAG
* * *
1368604 CTCAAGGCGTGAAGGGCTATCTATCAACCAAAACCTTCGAGTTTGATTACATTCAGCTC-AGGGA
1 CTCAAGGCGAGAAGGGCTATCTGTCAACCAAAACCTTCGAGTTCGATTACATTCAGCTCAAGGG-
* * *
1368668 CATGTCAAATTTTCAGCATAGCTCAAGGCGAGAAGGGCTATCT
65 CATATCAAATTTGCAGCATAGCTCAAGGCGAGAAGGGTTATCT
1368711 GTCAACAAAA
Statistics
Matches: 390, Mismatches: 47, Indels: 12
0.87 0.10 0.03
Matches are distributed among these distances:
335 70 0.18
336 5 0.01
337 287 0.74
338 2 0.01
339 26 0.07
ACGTcount: A:0.33, C:0.21, G:0.20, T:0.26
Consensus pattern (339 bp):
CTCAAGGCGAGAAGGGCTATCTGTCAACCAAAACCTTCGAGTTCGATTACATTCAGCTCAAGGGC
ATATCAAATTTGCAGCATAGCTCAAGGCGAGAAGGGTTATCTACCACAAACAAACCTTCGAGTTC
AATTACATTCAGCTCAAGGGCATATCAAATTCACAGCATAGCTCAAGGCGAGAAGGGATATCTAT
CAACAAAACTTCGAGTTCAATTCCATTCAGCTCAAGGGCGTATCAAATTTGCAGCAGAGCTCAAG
GCGAGAAGGGCTATATATCAACCAAAACCTTCGAGTTCAATTACATTCAGCTCAAGGGCATATCA
AATTTACAACATAG
Found at i:1369118 original size:17 final size:17
Alignment explanation
Indices: 1369096--1369128 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
1369086 ACCACTACCC
1369096 ACCTAATTACCTAACCT
1 ACCTAATTACCTAACCT
1369113 ACCTAATTACCTAACC
1 ACCTAATTACCTAACC
1369129 CACCATCATC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.36, C:0.36, G:0.00, T:0.27
Consensus pattern (17 bp):
ACCTAATTACCTAACCT
Found at i:1370035 original size:21 final size:20
Alignment explanation
Indices: 1370005--1370055 Score: 66
Period size: 21 Copynumber: 2.5 Consensus size: 20
1369995 TAGTTATTCA
*
1370005 TTTTTTTTAATTTGAGCATT
1 TTTTTTTTAATTTGAGCATG
*
1370025 TTTTGTTTTAATTTTAGCATG
1 TTTT-TTTTAATTTGAGCATG
1370046 TTTTATTTTA
1 TTTT-TTTTA
1370056 TTTATTTTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 4 0.15
21 23 0.85
ACGTcount: A:0.20, C:0.04, G:0.10, T:0.67
Consensus pattern (20 bp):
TTTTTTTTAATTTGAGCATG
Found at i:1370064 original size:15 final size:15
Alignment explanation
Indices: 1370046--1370102 Score: 59
Period size: 15 Copynumber: 3.9 Consensus size: 15
1370036 TTTTAGCATG
1370046 TTTTATTTTATTTAT
1 TTTTATTTTATTTAT
1370061 TTTTATTTT-TTTACT
1 TTTTATTTTATTTA-T
*
1370076 TCTTA--TTATTT-T
1 TTTTATTTTATTTAT
1370088 TTATTATTTTATTTA
1 TT-TTATTTTATTTA
1370103 ACATTTATTC
Statistics
Matches: 34, Mismatches: 2, Indels: 11
0.72 0.04 0.23
Matches are distributed among these distances:
12 2 0.06
13 5 0.15
14 7 0.21
15 20 0.59
ACGTcount: A:0.19, C:0.04, G:0.00, T:0.77
Consensus pattern (15 bp):
TTTTATTTTATTTAT
Found at i:1370095 original size:43 final size:41
Alignment explanation
Indices: 1370048--1370169 Score: 115
Period size: 43 Copynumber: 2.9 Consensus size: 41
1370038 TTAGCATGTT
* *
1370048 TTATTTTATTTATTTTTATTTTTTTACTTCTTATTATTT-TTTA
1 TTATTTTATTTATTTTTATTTTTTT-C-CCTT-TAATTTATTTA
**
1370091 TTATTTTATTTAACATTTATTCTTTTTCCCTTTAATTTATTTA
1 TTATTTTATTT-ATTTTTATT-TTTTTCCCTTTAATTTATTTA
* * *
1370134 ATATTTT-TTTATTTTTATATTTTT-CCTTTGATTTAT
1 TTATTTTATTTATTTTTATTTTTTTCCCTTTAATTTAT
1370170 ATAATATCTA
Statistics
Matches: 67, Mismatches: 9, Indels: 10
0.78 0.10 0.12
Matches are distributed among these distances:
39 11 0.16
40 5 0.07
41 6 0.09
42 8 0.12
43 24 0.36
44 8 0.12
45 5 0.07
ACGTcount: A:0.20, C:0.07, G:0.01, T:0.71
Consensus pattern (41 bp):
TTATTTTATTTATTTTTATTTTTTTCCCTTTAATTTATTTA
Found at i:1370162 original size:39 final size:43
Alignment explanation
Indices: 1370113--1370191 Score: 112
Period size: 39 Copynumber: 1.9 Consensus size: 43
1370103 ACATTTATTC
*
1370113 TTTTTCCCTTTAATTTATTTAATAT-T-TTT-TTATTTTTATA
1 TTTTTCCCTTTAATTTATATAATATCTATTTATTATTTTTATA
*
1370153 TTTTT-CCTTTGATTTATATAATATCTATTTATTATTTTT
1 TTTTTCCCTTTAATTTATATAATATCTATTTATTATTTTT
1370192 CGACTTTTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
39 17 0.50
40 6 0.18
41 3 0.09
42 8 0.24
ACGTcount: A:0.23, C:0.08, G:0.01, T:0.68
Consensus pattern (43 bp):
TTTTTCCCTTTAATTTATATAATATCTATTTATTATTTTTATA
Found at i:1370508 original size:320 final size:310
Alignment explanation
Indices: 1370056--1370645 Score: 887
Period size: 320 Copynumber: 1.9 Consensus size: 310
1370046 TTTTATTTTA
* * *
1370056 TTTATTTTTATTTTTTTACTTCTTATTATTTTTTATTATTTTATTTAACATTTATTCTTTTTCCC
1 TTTATTTTTATTATTTTACTTCTTATTATTTTTTATTACTTTATTTAACATTTATTATTTTTCCC
1370121 TTTAATTTATTTAATATTTTTTTATTTTTATATTTTTCCTTTGATTTATATAATATCTATTTATT
66 TTTAATTTATTTAATATTTTTTTATTTTTATATTTTTCCTTTGATTTATATAATATCTATTTATT
* *
1370186 ATTTTTCGACTTTTTAGGGATACTTTTCAACCAATCAAAGGTAATTAATTTGAATCGAATGTTTT
131 ATTTTTCAACTTTTTAGGGATACTTTTCAACCAATCAAAGGTAAGTAATTTGAATCGAATGTTTT
* * * *
1370251 TAATTTTAATTTTAATTTGAATTTTCGCAACTAAGACAACC-AGCAAATAAAATGGTACCGAAAG
196 AAATTTTAA-TTTAATTTAAATTTTCGCAACTAAGACAACCGA-AAAATAAAATGATACCGAAAG
1370315 GGAAATTCAAGGTAAGACAACCATCATTTTTTCTTTTTAATTTTAATATGTT
259 GGAAATTCAAGGTAAGACAACCATCATTTTTTCTTTTTAATTTTAATATGTT
*
1370367 TTTATTTTCT-TTATTTTACTTCTTATTATTTTTTTGATTACTTTATTTAACATTTTTTATTTTT
1 TTTATTTT-TATTATTTTACTTCTTATTA-TTTTTT-ATTACTTTATTTAACATTTATTATTTTT
* * * * *
1370431 GCCTTTGATTTATTTAATATTTAATATTTTTTCTTTTTCTTTTTTTTCCTTTGATTTATATAATA
63 CCCTTTAATTTATTT-A-A--T-AT-TTTTTTATTTTT-ATATTTTTCCTTTGATTTATATAATA
*
1370496 TCTATTTATTATTTTTCAACTTTTTAGGGATACTTTTCAACCAATCAAAGGTACGTAATTTGAAT
121 TCTATTTATTATTTTTCAACTTTTTAGGGATACTTTTCAACCAATCAAAGGTAAGTAATTTGAAT
*
1370561 CGAATGTTTTAAATTTTAATTTAATTTAAATTTTCGCAACTAAGACAACCGAAAAATTAAATGAT
186 CGAATGTTTTAAATTTTAATTTAATTTAAATTTTCGCAACTAAGACAACCGAAAAATAAAATGAT
* *
1370626 ACCGAAAGGGCAGTTCAAGG
251 ACCGAAAGGGAAATTCAAGG
1370646 GTGCTAATCC
Statistics
Matches: 249, Mismatches: 19, Indels: 14
0.88 0.07 0.05
Matches are distributed among these distances:
311 25 0.10
312 7 0.03
313 38 0.15
314 1 0.00
315 1 0.00
317 1 0.00
318 2 0.01
319 69 0.28
320 105 0.42
ACGTcount: A:0.29, C:0.11, G:0.08, T:0.52
Consensus pattern (310 bp):
TTTATTTTTATTATTTTACTTCTTATTATTTTTTATTACTTTATTTAACATTTATTATTTTTCCC
TTTAATTTATTTAATATTTTTTTATTTTTATATTTTTCCTTTGATTTATATAATATCTATTTATT
ATTTTTCAACTTTTTAGGGATACTTTTCAACCAATCAAAGGTAAGTAATTTGAATCGAATGTTTT
AAATTTTAATTTAATTTAAATTTTCGCAACTAAGACAACCGAAAAATAAAATGATACCGAAAGGG
AAATTCAAGGTAAGACAACCATCATTTTTTCTTTTTAATTTTAATATGTT
Found at i:1373925 original size:21 final size:21
Alignment explanation
Indices: 1373881--1373924 Score: 65
Period size: 19 Copynumber: 2.2 Consensus size: 21
1373871 ACACTATACA
1373881 TTTTGCATATGCATTTTTATT
1 TTTTGCATATGCATTTTTATT
*
1373902 TTTTGCA-ATGCA-TTTAATT
1 TTTTGCATATGCATTTTTATT
1373921 TTTT
1 TTTT
1373925 TGCACCGCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 10 0.45
20 5 0.23
21 7 0.32
ACGTcount: A:0.20, C:0.09, G:0.09, T:0.61
Consensus pattern (21 bp):
TTTTGCATATGCATTTTTATT
Found at i:1373928 original size:20 final size:21
Alignment explanation
Indices: 1373881--1373924 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 21
1373871 ACACTATACA
*
1373881 TTTTGCATATGCATTTTTATT
1 TTTTGCATATGCATTTATATT
1373902 TTTTGCA-ATGCATTTA-ATT
1 TTTTGCATATGCATTTATATT
1373921 TTTT
1 TTTT
1373925 TGCACCGCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 7 0.32
20 8 0.36
21 7 0.32
ACGTcount: A:0.20, C:0.09, G:0.09, T:0.61
Consensus pattern (21 bp):
TTTTGCATATGCATTTATATT
Found at i:1377230 original size:26 final size:26
Alignment explanation
Indices: 1377182--1377231 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
1377172 AAAACAAAAC
* *
1377182 ATATATATATATACATTTTAAAAATA
1 ATATATATATATACATGTAAAAAATA
1377208 ATATATATATATGA-ATGTAAAAAA
1 ATATATATATAT-ACATGTAAAAAA
1377232 ATATGTATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 20 0.95
27 1 0.05
ACGTcount: A:0.56, C:0.02, G:0.04, T:0.38
Consensus pattern (26 bp):
ATATATATATATACATGTAAAAAATA
Found at i:1379316 original size:105 final size:105
Alignment explanation
Indices: 1379123--1379558 Score: 710
Period size: 105 Copynumber: 4.1 Consensus size: 105
1379113 CCAATATCCT
**
1379123 TTGAAATTGGCTCTGAAATTAGGAAAATGTTCGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTT
1 TTGAAATTGGCTCTGAAATTAGGAAGTTGTT-GTTGACAACCAGCGGTCCCTTCGTCGTGAAGTT
1379188 GAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAG
65 GAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAG
* *
1379229 TTGAAATTGGCTCTGAAATTGGGAAGTTGTTGTTGACAACCAGAGGTCCCTTCGTCGTGAAGTTG
1 TTGAAATTGGCTCTGAAATTAGGAAGTTGTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTG
* * *
1379294 AACTTGCGTTTTTTGGATTCCAATATCCTTCGCTGTGAAG
66 AACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAG
* *
1379334 TTGAAATTGGCTCTGAAATTGGGAAGTTGTTGTTGACAACCAGTGGTCCCTTCGTCGTGAAGTTG
1 TTGAAATTGGCTCTGAAATTAGGAAGTTGTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTG
1379399 AACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAG
66 AACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAG
* * * *
1379439 TTAAAATTGGCTCTGAAATTAGGAAGTTATTATTGACAACCAGCGGTCCCTTCGTCGTGAAGGTG
1 TTGAAATTGGCTCTGAAATTAGGAAGTTGTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTG
* * *
1379504 AACTTGTGTTGTCTTGAGTTCAATATCCTTCGCTGTGAAG
66 AACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAG
*
1379544 TTGAAATTGACTCTG
1 TTGAAATTGGCTCTG
1379559 GCTAAAACTT
Statistics
Matches: 308, Mismatches: 22, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
105 280 0.91
106 28 0.09
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (105 bp):
TTGAAATTGGCTCTGAAATTAGGAAGTTGTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTG
AACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAG
Found at i:1390664 original size:11 final size:10
Alignment explanation
Indices: 1390639--1390663 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
1390629 ATAAGATAAG
1390639 AAAAATAATC
1 AAAAATAATC
1390649 AAAAATAATC
1 AAAAATAATC
1390659 AAAAA
1 AAAAA
1390664 AAGAAGTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.76, C:0.08, G:0.00, T:0.16
Consensus pattern (10 bp):
AAAAATAATC
Found at i:1391642 original size:20 final size:20
Alignment explanation
Indices: 1391614--1391651 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1391604 GGCCACCTCA
*
1391614 CCGGCCGCCGTTGATCGGCG
1 CCGGCCGCCGTTCATCGGCG
*
1391634 CCGGTCGCCGTTCATCGG
1 CCGGCCGCCGTTCATCGG
1391652 TGGCTAAACA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.05, C:0.39, G:0.37, T:0.18
Consensus pattern (20 bp):
CCGGCCGCCGTTCATCGGCG
Found at i:1395458 original size:77 final size:78
Alignment explanation
Indices: 1395371--1395516 Score: 183
Period size: 77 Copynumber: 1.9 Consensus size: 78
1395361 AAATAAAATA
*
1395371 TTATTTAATTAATT-CAAATTAAATAT-ACATCAAAA-ACTTATAATCTAAATTACAATCTT-TA
1 TTATTTAATT-ATTCCAAATTAAATATCA-ATCAAAAGA-GTATAATCTAAATTACAATCTTATA
1395432 ATGTTTATTTTAAAAC
63 ATGTTTATTTTAAAAC
* * * * *
1395448 TTATTTAATTATTCCGAATTATATATCAATTAAAAGAGTGTAATCTAAATTACATTCTTATAATG
1 TTATTTAATTATTCCAAATTAAATATCAATCAAAAGAGTATAATCTAAATTACAATCTTATAATG
1395513 TTTA
66 TTTA
1395517 CTTACTATAT
Statistics
Matches: 59, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
76 3 0.05
77 45 0.76
78 11 0.19
ACGTcount: A:0.42, C:0.10, G:0.04, T:0.44
Consensus pattern (78 bp):
TTATTTAATTATTCCAAATTAAATATCAATCAAAAGAGTATAATCTAAATTACAATCTTATAATG
TTTATTTTAAAAC
Found at i:1399338 original size:24 final size:24
Alignment explanation
Indices: 1399311--1399359 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
1399301 GTAAACGGAG
*
1399311 ATATCAAAAATCAAAACATAATTC
1 ATATCAAAAATCAAAACAGAATTC
* * *
1399335 ATATCAGATATCAGAACAGAATTC
1 ATATCAAAAATCAAAACAGAATTC
1399359 A
1 A
1399360 GGTAACGTAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.53, C:0.16, G:0.06, T:0.24
Consensus pattern (24 bp):
ATATCAAAAATCAAAACAGAATTC
Found at i:1401847 original size:18 final size:18
Alignment explanation
Indices: 1401824--1401918 Score: 119
Period size: 18 Copynumber: 5.6 Consensus size: 18
1401814 CAACGGTCAA
*
1401824 CGGGTCGAGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
*
1401842 CGGGTCGGGTCAATGGGT
1 CGGGTCGGGTCAACGGGT
1401860 CGGGTCGGGTCAA-----
1 CGGGTCGGGTCAACGGGT
* *
1401873 CGGGTCAGGTAAACGGGT
1 CGGGTCGGGTCAACGGGT
1401891 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
1401909 CGGGTCGGGT
1 CGGGTCGGGT
1401919 TGTGACCGGT
Statistics
Matches: 66, Mismatches: 6, Indels: 10
0.80 0.07 0.12
Matches are distributed among these distances:
13 11 0.17
18 55 0.83
ACGTcount: A:0.14, C:0.20, G:0.48, T:0.18
Consensus pattern (18 bp):
CGGGTCGGGTCAACGGGT
Found at i:1401872 original size:49 final size:49
Alignment explanation
Indices: 1401818--1401918 Score: 168
Period size: 49 Copynumber: 2.1 Consensus size: 49
1401808 GACGTTCAAC
* *
1401818 GGTCAACGGGTC-GAGTCAACGGGTCGGGTCGGGTCAATGGGTCGGGTCG
1 GGTCAACGGGTCAG-GTAAACGGGTCGGGTCGGGTCAACGGGTCGGGTCG
1401867 GGTCAACGGGTCAGGTAAACGGGTCGGGTCGGGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCAGGTAAACGGGTCGGGTCGGGTCAACGGGTCGGGTCG
1401916 GGT
1 GGT
1401919 TGTGACCGGT
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
49 48 0.98
50 1 0.02
ACGTcount: A:0.15, C:0.20, G:0.48, T:0.18
Consensus pattern (49 bp):
GGTCAACGGGTCAGGTAAACGGGTCGGGTCGGGTCAACGGGTCGGGTCG
Found at i:1401877 original size:31 final size:31
Alignment explanation
Indices: 1401842--1401914 Score: 119
Period size: 31 Copynumber: 2.4 Consensus size: 31
1401832 GTCAACGGGT
*
1401842 CGGGTCGGGTCAATGGGTCGGGTCGGGTCAA
1 CGGGTCGGGTCAACGGGTCGGGTCGGGTCAA
* *
1401873 CGGGTCAGGTAAACGGGTCGGGTCGGGTCAA
1 CGGGTCGGGTCAACGGGTCGGGTCGGGTCAA
1401904 CGGGTCGGGTC
1 CGGGTCGGGTC
1401915 GGGTTGTGAC
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.14, C:0.21, G:0.48, T:0.18
Consensus pattern (31 bp):
CGGGTCGGGTCAACGGGTCGGGTCGGGTCAA
Found at i:1401914 original size:13 final size:13
Alignment explanation
Indices: 1401818--1401896 Score: 62
Period size: 13 Copynumber: 6.3 Consensus size: 13
1401808 GACGTTCAAC
1401818 GGTCAACGGGTCG
1 GGTCAACGGGTCG
*
1401831 AGTCAACGGGTCG
1 GGTCAACGGGTCG
1401844 GGT---CGGGTCAATG
1 GGTCAACGGGTC---G
1401857 GGT---CGGGTCG
1 GGTCAACGGGTCG
*
1401867 GGTCAACGGGTCA
1 GGTCAACGGGTCG
*
1401880 GGTAAACGGGTCG
1 GGTCAACGGGTCG
1401893 GGTC
1 GGTC
1401897 GGGTCAACGG
Statistics
Matches: 54, Mismatches: 6, Indels: 12
0.75 0.08 0.17
Matches are distributed among these distances:
10 10 0.19
13 44 0.81
ACGTcount: A:0.16, C:0.20, G:0.46, T:0.18
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:1404060 original size:24 final size:23
Alignment explanation
Indices: 1404032--1404133 Score: 91
Period size: 24 Copynumber: 4.3 Consensus size: 23
1404022 AGATATCAAA
* *
1404032 AATCAAAACATAATTCATATCAG
1 AATCAGAACAGAATTCATATCAG
* *
1404055 ATATCAGAACAGAATCCAGATCAG
1 A-ATCAGAACAGAATTCATATCAG
*
1404079 AATCAGAACAGAATTCAGGTAAC-G
1 AATCAGAACAGAATTCA--TATCAG
*
1404103 TATCAGAACAGAATTCA-ATTCAG
1 AATCAGAACAGAATTCATA-TCAG
1404126 AAATCAGA
1 -AATCAGA
1404134 TAAAATATTT
Statistics
Matches: 63, Mismatches: 10, Indels: 11
0.75 0.12 0.13
Matches are distributed among these distances:
21 1 0.02
22 1 0.02
23 17 0.27
24 42 0.67
25 2 0.03
ACGTcount: A:0.48, C:0.18, G:0.14, T:0.21
Consensus pattern (23 bp):
AATCAGAACAGAATTCATATCAG
Found at i:1404074 original size:12 final size:11
Alignment explanation
Indices: 1404052--1404116 Score: 60
Period size: 12 Copynumber: 5.5 Consensus size: 11
1404042 TAATTCATAT
1404052 CAGATATCAGAA
1 CAGA-ATCAGAA
*
1404064 CAGAATCCAGAT
1 CAGAAT-CAGAA
1404076 CAGAATCAGAA
1 CAGAATCAGAA
1404087 CAGAATTCAGGTAA
1 CAGAA-TCA-G-AA
*
1404101 C-GTATCAGAA
1 CAGAATCAGAA
1404111 CAGAAT
1 CAGAAT
1404117 TCAATTCAGA
Statistics
Matches: 44, Mismatches: 4, Indels: 11
0.75 0.07 0.19
Matches are distributed among these distances:
10 3 0.07
11 15 0.34
12 20 0.45
13 3 0.07
14 3 0.07
ACGTcount: A:0.46, C:0.18, G:0.18, T:0.17
Consensus pattern (11 bp):
CAGAATCAGAA
Found at i:1406572 original size:13 final size:13
Alignment explanation
Indices: 1406554--1406578 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1406544 ACGGTCAACG
1406554 GTCAACGGGTCGA
1 GTCAACGGGTCGA
1406567 GTCAACGGGTCG
1 GTCAACGGGTCG
1406579 GGTCGGGTCA
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:0.20, C:0.24, G:0.40, T:0.16
Consensus pattern (13 bp):
GTCAACGGGTCGA
Found at i:1406594 original size:13 final size:13
Alignment explanation
Indices: 1406577--1406626 Score: 82
Period size: 13 Copynumber: 3.8 Consensus size: 13
1406567 GTCAACGGGT
1406577 CGGGTCGGGTCAA
1 CGGGTCGGGTCAA
* *
1406590 TGGGTCGGGTAAA
1 CGGGTCGGGTCAA
1406603 CGGGTCGGGTCAA
1 CGGGTCGGGTCAA
1406616 CGGGTCGGGTC
1 CGGGTCGGGTC
1406627 GGGTTGTGAC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 33 1.00
ACGTcount: A:0.14, C:0.20, G:0.48, T:0.18
Consensus pattern (13 bp):
CGGGTCGGGTCAA
Found at i:1406595 original size:31 final size:31
Alignment explanation
Indices: 1406553--1406613 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
1406543 GACGGTCAAC
*
1406553 GGTCAACGGGTCGAGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGAGTAAACGGGTCGGGTCG
* *
1406584 GGTCAATGGGTCGGGTAAACGGGTCGGGTC
1 GGTCAACGGGTCGAGTAAACGGGTCGGGTC
1406614 AACGGGTCGG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.16, C:0.20, G:0.46, T:0.18
Consensus pattern (31 bp):
GGTCAACGGGTCGAGTAAACGGGTCGGGTCG
Found at i:1406613 original size:18 final size:18
Alignment explanation
Indices: 1406559--1406599 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
1406549 CAACGGTCAA
*
1406559 CGGGTCGAGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
*
1406577 CGGGTCGGGTCAATGGGT
1 CGGGTCGGGTCAACGGGT
1406595 CGGGT
1 CGGGT
1406600 AAACGGGTCG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.12, C:0.20, G:0.49, T:0.20
Consensus pattern (18 bp):
CGGGTCGGGTCAACGGGT
Found at i:1407658 original size:81 final size:81
Alignment explanation
Indices: 1407523--1407759 Score: 350
Period size: 81 Copynumber: 2.9 Consensus size: 81
1407513 TTTTAAGGTG
* *
1407523 AAAGATTAAATGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGT
1 AAAGATTAAATGCCTAGCTGTGCATTTGACAAAAAGGTGTCAATTATGCAAGTTAGATGAAAGGT
*
1407588 TAAATATCTTTGAGTT
66 TAAATACCTTTGAGTT
* * * * *
1407604 AAAGATTAAATGCCTAGTTGTGCATTTGACATAAAGGTGACAATTATGAAAGTTAGATAAAAGGT
1 AAAGATTAAATGCCTAGCTGTGCATTTGACAAAAAGGTGTCAATTATGCAAGTTAGATGAAAGGT
1407669 TAAATACCTTTGAGTT
66 TAAATACCTTTGAGTT
* * *
1407685 AAAGATTAAATGACTAGCTATGCATTTGACAAAAAAAGTGTCAATTATGCCAA-TTAGATGAAAG
1 AAAGATTAAATGCCTAGCTGTGCATTTGAC-AAAAAGGTGTCAATTATG-CAAGTTAGATGAAAG
1407749 GTTAAATACCT
64 GTTAAATACCT
1407760 AGATGTGCAT
Statistics
Matches: 139, Mismatches: 15, Indels: 3
0.89 0.10 0.02
Matches are distributed among these distances:
81 101 0.73
82 36 0.26
83 2 0.01
ACGTcount: A:0.39, C:0.11, G:0.19, T:0.31
Consensus pattern (81 bp):
AAAGATTAAATGCCTAGCTGTGCATTTGACAAAAAGGTGTCAATTATGCAAGTTAGATGAAAGGT
TAAATACCTTTGAGTT
Found at i:1407772 original size:60 final size:59
Alignment explanation
Indices: 1407705--1407818 Score: 165
Period size: 59 Copynumber: 1.9 Consensus size: 59
1407695 TGACTAGCTA
*
1407705 TGCATTTGACAAAAAAAGTGTCAATTATGCCAATTAGATGAAAGGTTAAATACCTAGATG
1 TGCATTTGA-AAAAAAAGTGTCAATTATACCAATTAGATGAAAGGTTAAATACCTAGATG
* * * * *
1407765 TGCATTTGATAGAAAAGTGTCAATTATACTAGTTAGATGAAATGTTAAATACCT
1 TGCATTTGAAAAAAAAGTGTCAATTATACCAATTAGATGAAAGGTTAAATACCT
1407819 TTGAGTTAAA
Statistics
Matches: 48, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
59 39 0.81
60 9 0.19
ACGTcount: A:0.40, C:0.11, G:0.18, T:0.32
Consensus pattern (59 bp):
TGCATTTGAAAAAAAAGTGTCAATTATACCAATTAGATGAAAGGTTAAATACCTAGATG
Found at i:1407885 original size:81 final size:81
Alignment explanation
Indices: 1407745--1408314 Score: 791
Period size: 81 Copynumber: 7.2 Consensus size: 81
1407735 CAATTAGATG
* * * * * * * *
1407745 AAAGGTTAAATACCTAGATGTGCATTTGATAGAAAAGTGTCAATTATACTAGTTAGATGAAATGT
1 AAAGATTAAATGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGT
1407810 TAAATACCTTTGAGTT
66 TAAATACCTTTGAGTT
* *
1407826 AAAGATTAAATGTCTAGCTGTGCATTTGACATAAAGGTGTCAATTATGCCAGTTAGATGAAAGGT
1 AAAGATTAAATGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGT
1407891 TAAATACCTTTGAGTT
66 TAAATACCTTTGAGTT
* *
1407907 AAAGATTAAATGCCTAG-T-T--A--T-ATA-AAA-GTGTCAA-TATGCCAATTAGATGAAAGGT
1 AAAGATTAAATGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGT
1407962 TAAATACCTTTGAGTT
66 TAAATACCTTTGAGTT
* * * *
1407978 AAAGATTAAATGCCTAGCTGTGCATTTCACAAAAAGGTGTTAATTATGCCAGTTAGGTGAAAGGT
1 AAAGATTAAATGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGT
1408043 TAAATACCTTTGAGTT
66 TAAATACCTTTGAGTT
* *
1408059 AAAGATTAAATGCCTAGCTGTGCATTTGACAGAAAGATGTCAATTATGCCAGTTAGATGAAATGT
1 AAAGATTAAATGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGT
*
1408124 TAAATACTTTTGAGTT
66 TAAATACCTTTGAGTT
** * *
1408140 AAAGATTAAATGCCTAGCTGCACATTTGATAGAAAGGTGTCAATTATGCAAGTTAGATGAAAGGT
1 AAAGATTAAATGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGT
1408205 TAAATACCTTTGAGTT
66 TAAATACCTTTGAGTT
* * * *
1408221 AAAGATTAAATGCCTAGCCGTGCATTTGGCAGAAAGGTGCCAATCATGCCAGTTAGATGAAAGGT
1 AAAGATTAAATGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGT
* * *
1408286 TAAATGCCTATGAGTA
66 TAAATACCTTTGAGTT
*
1408302 AAAGTTTAAATGC
1 AAAGATTAAATGC
1408315 TTAACAGTGA
Statistics
Matches: 436, Mismatches: 43, Indels: 20
0.87 0.09 0.04
Matches are distributed among these distances:
71 53 0.12
72 8 0.02
73 4 0.01
74 2 0.00
75 2 0.00
77 2 0.00
78 2 0.00
79 4 0.01
80 7 0.02
81 352 0.81
ACGTcount: A:0.37, C:0.11, G:0.20, T:0.32
Consensus pattern (81 bp):
AAAGATTAAATGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGT
TAAATACCTTTGAGTT
Found at i:1410950 original size:65 final size:63
Alignment explanation
Indices: 1410872--1411031 Score: 205
Period size: 65 Copynumber: 2.5 Consensus size: 63
1410862 AATTAAATTG
*
1410872 AACATCGAATGCATTTCATGCATCGATGCACATACCATGCACCGATGCACTGAGGAT-TTTATGA
1 AACATCGAATGCATTTGATGCATCGATGCACA-ACCATGCACCGATGCACTGAGGATATTT-TG-
1410936 A
63 A
* * ** *
1410937 AACATCGAATGCATTTGATGCATCGATGCACCAGCCATGCATCGATGCACTTTGGCTATTTTGA
1 AACATCGAATGCATTTGATGCATCGATGCA-CAACCATGCACCGATGCACTGAGGATATTTTGA
* *
1411001 AACATCGAATACACTTGATGCATCGATGCAC
1 AACATCGAATGCATTTGATGCATCGATGCAC
1411032 GCTTAGTGTA
Statistics
Matches: 85, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
63 1 0.01
64 29 0.34
65 50 0.59
66 5 0.06
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.27
Consensus pattern (63 bp):
AACATCGAATGCATTTGATGCATCGATGCACAACCATGCACCGATGCACTGAGGATATTTTGA
Found at i:1419583 original size:64 final size:65
Alignment explanation
Indices: 1419476--1419685 Score: 250
Period size: 65 Copynumber: 3.2 Consensus size: 65
1419466 TTTTTCAGAG
* *
1419476 TGATGCACCGATGCACCAATCCATGCATCGATGCAC-CATGAATTAAATTG-AACATCGAATGCA
1 TGATGCATCGATGCACCAA-CCATGCATCGATGCACTCA-GAATTATATTGAAACATCGAATGCA
1419539 TT
64 TT
* * * *
1419541 TCATGCATCGATGCA-CATACCATGCACCGATGCACTGAGAATTTTA-TGAAAACATCGAATGCA
1 TGATGCATCGATGCACCA-ACCATGCATCGATGCACTCAGAATTATATTG-AAACATCGAATGCA
1419604 TT
64 TT
* ** * *
1419606 TGATGCATCGATGCACCAACCATGCATCGATGCACTCTG-GCTATTTTGAAACATCGAATGCACT
1 TGATGCATCGATGCACCAACCATGCATCGATGCACTCAGAATTATATTGAAACATCGAATGCATT
1419670 TGATGCATCGATGCAC
1 TGATGCATCGATGCAC
1419686 GCTTAGTGCA
Statistics
Matches: 124, Mismatches: 15, Indels: 13
0.82 0.10 0.09
Matches are distributed among these distances:
63 2 0.02
64 56 0.45
65 64 0.52
66 2 0.02
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.26
Consensus pattern (65 bp):
TGATGCATCGATGCACCAACCATGCATCGATGCACTCAGAATTATATTGAAACATCGAATGCATT
Found at i:1423826 original size:81 final size:81
Alignment explanation
Indices: 1423683--1424082 Score: 543
Period size: 81 Copynumber: 4.9 Consensus size: 81
1423673 TTTTAAGATG
* * * * * *
1423683 AAAGATTAAATGCCTAGTTGTGCCTTTGATATAAAGGTGTCAATTATGCCAGTTAGAAGAAAGGT
1 AAAGATTAAATGCCTAGATGTGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATGAAAGGT
* *
1423748 TAAATAACTTTGAGAT
66 TAAATACCTTTGAGTT
*
1423764 AAATATTAAATGCCTAGATGTGCATTTGACA-AATATGTGTCAATTATGCCAGTTAGATGAAAGG
1 AAAGATTAAATGCCTAGATGTGCATTTGACAGAA-ATGTGTCAATTATGCCAGTTAGATGAAAGG
* *
1423828 TTAACTACCATTGAGTT
65 TTAAATACCTTTGAGTT
*
1423845 AAAGATTAAATGCCTA-ACTGTGTATTTGACAGAAATGTGTCAATTATGCCAGTTAGATGAAAGG
1 AAAGATTAAATGCCTAGA-TGTGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATGAAAGG
1423909 TTAAATACCTTTGAGTT
65 TTAAATACCTTTGAGTT
* * * * * * * * *
1423926 AAATATTAAATCCCTTGTTATGTATTTGACAGAAATATGTCAATTATGCCAGTTGGATGAAATGT
1 AAAGATTAAATGCCTAGATGTGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATGAAAGGT
1423991 TAAATACCTTTGAGTT
66 TAAATACCTTTGAGTT
* * *
1424007 AAAGATTAAATGTCTAGCTGTGCATTTGACAGAAATGTGTCAATTATGCCAATTAGATGAAAGGT
1 AAAGATTAAATGCCTAGATGTGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATGAAAGGT
*
1424072 CAAATACCTTT
66 TAAATACCTTT
1424083 ACCTAGTTGT
Statistics
Matches: 281, Mismatches: 34, Indels: 8
0.87 0.11 0.02
Matches are distributed among these distances:
80 3 0.01
81 276 0.98
82 2 0.01
ACGTcount: A:0.36, C:0.12, G:0.19, T:0.34
Consensus pattern (81 bp):
AAAGATTAAATGCCTAGATGTGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATGAAAGGT
TAAATACCTTTGAGTT
Found at i:1423955 original size:162 final size:162
Alignment explanation
Indices: 1423683--1424327 Score: 795
Period size: 162 Copynumber: 4.1 Consensus size: 162
1423673 TTTTAAGATG
* * * * *
1423683 AAAGATTAAATGCCTAGTTGTGCCTTTGATATAAAGGTGTCAATTATGCCAGTTAGAAGAAAGGT
1 AAAGATTAAATGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGT
* * * *
1423748 TAAATAACTTTGAGATAAATATTAAATGCCTAGATGTGCATTTGACA-AATATGTGTCAATTATG
66 TAAATACCTTTGAGTTAAATATTAAATGCCTAGTTGTGTATTTGACAGAA-ATGTGTCAATTATG
* *
1423812 CCAGTTAGATGAAAGGTTAACTACCATTGAGTT
130 CCAGTTAGATGAAAGGTTAAATACCTTTGAGTT
* * *
1423845 AAAGATTAAATGCCTAACTGTGTATTTGACAGAAATGTGTCAATTATGCCAGTTAGATGAAAGGT
1 AAAGATTAAATGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGT
* * * *
1423910 TAAATACCTTTGAGTTAAATATTAAATCCCTTGTTATGTATTTGACAGAAATATGTCAATTATGC
66 TAAATACCTTTGAGTTAAATATTAAATGCCTAGTTGTGTATTTGACAGAAATGTGTCAATTATGC
* *
1423975 CAGTTGGATGAAATGTTAAATACCTTTGAGTT
131 CAGTTAGATGAAAGGTTAAATACCTTTGAGTT
* * *
1424007 AAAGATTAAATGTCTAGCTGTGCATTTGACAGAAATGTGTCAATTATGCCAATTAGATGAAAGGT
1 AAAGATTAAATGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGT
* *
1424072 CAAATACC-----------T-TT--A--CCTAGTTGTGTATTTGACA-AAAAGATGTCAATTATG
66 TAAATACCTTTGAGTTAAATATTAAATGCCTAGTTGTGTATTTGACAGAAATG-TGTCAATTATG
* *
1424120 CTAGTTAGATGAAAGGTTAAGTACCTTTGAGTT
130 CCAGTTAGATGAAAGGTTAAATACCTTTGAGTT
* *
1424153 AAAGATTAAATGCCTAGCTGTGCATTTGATAAAAAGGTGTCAATTATGCCAGTTAGATGAAAGGT
1 AAAGATTAAATGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGT
* * ** * * *
1424218 TAAATACCTTTGAGTTAAAGATTAAATGCCTAGCTGTGTATTTGGTAGAAAGGTGCCAATCATGC
66 TAAATACCTTTGAGTTAAATATTAAATGCCTAGTTGTGTATTTGACAGAAATGTGTCAATTATGC
* * *
1424283 CAGTTAGATAAAAGGTTAAATGCCTTTGAGTA
131 CAGTTAGATGAAAGGTTAAATACCTTTGAGTT
1424315 AAAGATTAAATGC
1 AAAGATTAAATGC
1424328 TTAACAGTGT
Statistics
Matches: 413, Mismatches: 51, Indels: 38
0.82 0.10 0.08
Matches are distributed among these distances:
145 3 0.01
146 124 0.30
148 1 0.00
150 2 0.00
151 1 0.00
158 2 0.00
160 1 0.00
162 273 0.66
163 6 0.01
ACGTcount: A:0.36, C:0.11, G:0.20, T:0.33
Consensus pattern (162 bp):
AAAGATTAAATGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGT
TAAATACCTTTGAGTTAAATATTAAATGCCTAGTTGTGTATTTGACAGAAATGTGTCAATTATGC
CAGTTAGATGAAAGGTTAAATACCTTTGAGTT
Found at i:1424134 original size:65 final size:65
Alignment explanation
Indices: 1424020--1424147 Score: 177
Period size: 65 Copynumber: 2.0 Consensus size: 65
1424010 GATTAAATGT
*
1424020 CTAGCTGTGCATTTGACAGAAATGTGTCAATTATGCCAATTAGATGAAAGGTCAAATACCTTTAC
1 CTAGCTGTGCATTTGACAGAAAAGTGTCAATTATGCCAATTAGATGAAAGGTCAAATACCTTTAC
* * * * * *
1424085 CTAGTTGTGTATTTGACA-AAAAGATGTCAATTATGCTAGTTAGATGAAAGGTTAAGTACCTTT
1 CTAGCTGTGCATTTGACAGAAAAG-TGTCAATTATGCCAATTAGATGAAAGGTCAAATACCTTT
1424148 GAGTTAAAGA
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
64 4 0.07
65 51 0.93
ACGTcount: A:0.34, C:0.13, G:0.20, T:0.34
Consensus pattern (65 bp):
CTAGCTGTGCATTTGACAGAAAAGTGTCAATTATGCCAATTAGATGAAAGGTCAAATACCTTTAC
Found at i:1424210 original size:146 final size:146
Alignment explanation
Indices: 1423946--1424228 Score: 458
Period size: 146 Copynumber: 1.9 Consensus size: 146
1423936 TCCCTTGTTA
* * * *
1423946 TGTATTTGACAGAAATATGTCAATTATGCCAGTTGGATGAAATGTTAAATACCTTTGAGTTAAAG
1 TGTATTTGACAAAAAGATGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTTAAAG
* * *
1424011 ATTAAATGTCTAGCTGTGCATTTGACAGAAATGTGTCAATTATGCCAATTAGATGAAAGGTCAAA
66 ATTAAATGCCTAGCTGTGCATTTGACAAAAAGGTGTCAATTATGCCAATTAGATGAAAGGTCAAA
1424076 TACCTTTACCTAGTTG
131 TACCTTTACCTAGTTG
* *
1424092 TGTATTTGACAAAAAGATGTCAATTATGCTAGTTAGATGAAAGGTTAAGTACCTTTGAGTTAAAG
1 TGTATTTGACAAAAAGATGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTTAAAG
* * *
1424157 ATTAAATGCCTAGCTGTGCATTTGATAAAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAA
66 ATTAAATGCCTAGCTGTGCATTTGACAAAAAGGTGTCAATTATGCCAATTAGATGAAAGGTCAAA
1424222 TACCTTT
131 TACCTTT
1424229 GAGTTAAAGA
Statistics
Matches: 125, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
146 125 1.00
ACGTcount: A:0.35, C:0.11, G:0.20, T:0.34
Consensus pattern (146 bp):
TGTATTTGACAAAAAGATGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTTAAAG
ATTAAATGCCTAGCTGTGCATTTGACAAAAAGGTGTCAATTATGCCAATTAGATGAAAGGTCAAA
TACCTTTACCTAGTTG
Found at i:1424219 original size:81 final size:81
Alignment explanation
Indices: 1424084--1424327 Score: 371
Period size: 81 Copynumber: 3.0 Consensus size: 81
1424074 AATACCTTTA
* * * * *
1424084 CCTAGTTGTGTATTTGACAAAAAGATGTCAATTATGCTAGTTAGATGAAAGGTTAAGTACCTTTG
1 CCTAGCTGTGTATTTGATAAAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCTTTG
1424149 AGTTAAAGATTAAATG
66 AGTTAAAGATTAAATG
*
1424165 CCTAGCTGTGCATTTGATAAAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCTTTG
1 CCTAGCTGTGTATTTGATAAAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCTTTG
1424230 AGTTAAAGATTAAATG
66 AGTTAAAGATTAAATG
* * * * * *
1424246 CCTAGCTGTGTATTTGGTAGAAAGGTGCCAATCATGCCAGTTAGATAAAAGGTTAAATGCCTTTG
1 CCTAGCTGTGTATTTGATAAAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCTTTG
*
1424311 AGTAAAAGATTAAATG
66 AGTTAAAGATTAAATG
1424327 C
1 C
1424328 TTAACAGTGT
Statistics
Matches: 149, Mismatches: 14, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
81 149 1.00
ACGTcount: A:0.35, C:0.11, G:0.22, T:0.32
Consensus pattern (81 bp):
CCTAGCTGTGTATTTGATAAAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCTTTG
AGTTAAAGATTAAATG
Found at i:1424305 original size:23 final size:22
Alignment explanation
Indices: 1424286--1424327 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
1424276 ATCATGCCAG
*
1424286 TTAGA-TAAAAGGTTAAATGCC
1 TTAGAGTAAAAGATTAAATGCC
*
1424307 TTTGAGTAAAAGATTAAATGC
1 TTAGAGTAAAAGATTAAATGC
1424328 TTAACAGTGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.43, C:0.07, G:0.19, T:0.31
Consensus pattern (22 bp):
TTAGAGTAAAAGATTAAATGCC
Found at i:1427289 original size:37 final size:37
Alignment explanation
Indices: 1427239--1427432 Score: 232
Period size: 37 Copynumber: 5.3 Consensus size: 37
1427229 ACTTTCTAAA
1427239 CAAATCAATCTTAAGCCTTCACGG-AGAAGTAGTGAAG
1 CAAATCAATCTTAAGCCTTCACGGAAG-AGTAGTGAAG
**
1427276 CAAATCAATCTTAAGCCTTCACAAAAGAGTAGTGAAG
1 CAAATCAATCTTAAGCCTTCACGGAAGAGTAGTGAAG
* ** *
1427313 CAAGTCAATCTTAAGCCTTCACAAAATAGTAGTGAAG
1 CAAATCAATCTTAAGCCTTCACGGAAGAGTAGTGAAG
* ** * *
1427350 CAAGTCAATCTTAAGCC-TCGTGGAAGATTAGGGAAG
1 CAAATCAATCTTAAGCCTTCACGGAAGAGTAGTGAAG
* *
1427386 CAAATCAATCTT-AGCCTTCAAGGAAGAGTAGTAAAG
1 CAAATCAATCTTAAGCCTTCACGGAAGAGTAGTGAAG
*
1427422 AAAATCAATCT
1 CAAATCAATCT
1427433 CGAGTCTGGT
Statistics
Matches: 137, Mismatches: 18, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
35 4 0.03
36 47 0.34
37 84 0.61
38 2 0.01
ACGTcount: A:0.40, C:0.18, G:0.19, T:0.23
Consensus pattern (37 bp):
CAAATCAATCTTAAGCCTTCACGGAAGAGTAGTGAAG
Found at i:1427680 original size:166 final size:164
Alignment explanation
Indices: 1427479--1427805 Score: 388
Period size: 166 Copynumber: 2.0 Consensus size: 164
1427469 CTCATTTTCT
* * * * *
1427479 GAAGATTGTTCAAGTCCTATACTCCCTGGAAGAAGAGGGAGAAGA-CTTGTTT-TATGAAGATTA
1 GAAGATTGTTCAAGTCCTATACTCCCTGAAAGAAGAGGGAGAAGACCTT-TTTCCA-AAAAAAT-
* * * *
1427542 TTCAAGTCCTATACTCCCTAAAAGAAGAGGGAGCGGATCTGTTTGCCGAAGATTTTTTCAAGTCC
63 TTCAAGTCCTATACTCCCTAAAAGAAGAGGGAGCAGACCCGTTTGCCGAAGA-TTGTTCAAGTCC
* *
1427607 TATACTCATTGAAAGAAGAAGGAGCGGTCCCGTTTGCC
127 TATAATCATTGAAAGAAGAAGGAGCGGACCCGTTTGCC
** * *
1427645 GAAGATTGTTTGAGTCTTATACTCCCTGAAAGAAGAGGGAGCAGACCCTTTTTCCAAAAAAATTT
1 GAAGATTGTTCAAGTCCTATACTCCCTGAAAGAAGAGGGAGAAGA-CCTTTTTCCAAAAAAATTT
* * ** *
1427710 CAAGTCTTATACTCCCTGAAAGAAGAGGGAGCAGACCCGTTTTTCGAAGATTGTTCGAGTCCTAT
65 CAAGTCCTATACTCCCTAAAAGAAGAGGGAGCAGACCCGTTTGCCGAAGATTGTTCAAGTCCTAT
* * *
1427775 AATCCTTGAACGAAGATGGAGCGGACCCGTT
130 AATCATTGAAAGAAGAAGGAGCGGACCCGTT
1427806 CTTCAAAGAT
Statistics
Matches: 135, Mismatches: 23, Indels: 7
0.82 0.14 0.04
Matches are distributed among these distances:
165 39 0.29
166 85 0.63
167 7 0.05
168 4 0.03
ACGTcount: A:0.30, C:0.19, G:0.24, T:0.27
Consensus pattern (164 bp):
GAAGATTGTTCAAGTCCTATACTCCCTGAAAGAAGAGGGAGAAGACCTTTTTCCAAAAAAATTTC
AAGTCCTATACTCCCTAAAAGAAGAGGGAGCAGACCCGTTTGCCGAAGATTGTTCAAGTCCTATA
ATCATTGAAAGAAGAAGGAGCGGACCCGTTTGCC
Found at i:1427802 original size:55 final size:55
Alignment explanation
Indices: 1427473--1427825 Score: 325
Period size: 55 Copynumber: 6.4 Consensus size: 55
1427463 AGCAGACTCA
* * **
1427473 TTTTCTGAAGATTGTTCAAGTCCTATACTCCCTGGAAGAAGAGGGAGAAGACTTGT
1 TTTTC-GAAGATTGTTCAAGTCCTATACTCCCTGAAAGAAGAGGGAGCAGACCCGT
* * * * *
1427529 TTTAT-GAAGATTATTCAAGTCCTATACTCCCTAAAAGAAGAGGGAGCGGATCTGT
1 TTT-TCGAAGATTGTTCAAGTCCTATACTCCCTGAAAGAAGAGGGAGCAGACCCGT
** * ** * * *
1427584 TTGCCGAAGATTTTTTCAAGTCCTATACTCATTGAAAGAAGAAGGAGCGGTCCCGT
1 TTTTCGAAGA-TTGTTCAAGTCCTATACTCCCTGAAAGAAGAGGGAGCAGACCCGT
** ** *
1427640 TTGCCGAAGATTGTTTGAGTCTTATACTCCCTGAAAGAAGAGGGAGCAGACCC-T
1 TTTTCGAAGATTGTTCAAGTCCTATACTCCCTGAAAGAAGAGGGAGCAGACCCGT
* * * *
1427694 TTTTCCAAAAAAAT-TTCAAGTCTTATACTCCCTGAAAGAAGAGGGAGCAGACCCGT
1 TTTT-C-GAAGATTGTTCAAGTCCTATACTCCCTGAAAGAAGAGGGAGCAGACCCGT
* * * * * *
1427750 TTTTCGAAGATTGTTCGAGTCCTATAATCCTTGAACGAAGATGGAGCGGACCCGT
1 TTTTCGAAGATTGTTCAAGTCCTATACTCCCTGAAAGAAGAGGGAGCAGACCCGT
* * *
1427805 TCTTCAAAGATTTTTCAAGTC
1 TTTTCGAAGATTGTTCAAGTC
1427826 TCACTTATTC
Statistics
Matches: 243, Mismatches: 47, Indels: 15
0.80 0.15 0.05
Matches are distributed among these distances:
54 7 0.03
55 176 0.72
56 59 0.24
57 1 0.00
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.29
Consensus pattern (55 bp):
TTTTCGAAGATTGTTCAAGTCCTATACTCCCTGAAAGAAGAGGGAGCAGACCCGT
Found at i:1427826 original size:110 final size:109
Alignment explanation
Indices: 1427480--1427825 Score: 361
Period size: 110 Copynumber: 3.1 Consensus size: 109
1427470 TCATTTTCTG
* * * ** *
1427480 AAGATTGTTCAAGTCCTATACTCCCTGGAAGAAGAGGGAGAAGACTTGTTTTAT-GAAGATTATT
1 AAGATTTTTCAAGTCCTATACTCCCTGAAAGAAGAGGGAGCAGACCCGTTTT-TCGAAGATTGTT
* * * * * *
1427544 CAAGTCCTATACTCCCTAAAAGAAGAGGGAGCGGATCTGTTTGCCG
65 CGAGTCCTATACTCCCTGAAAGAAGAGGGAGCGGACCCGTTT-TCA
** * * * **
1427590 AAGATTTTTTCAAGTCCTATACTCATTGAAAGAAGAAGGAGCGGTCCCGTTTGCCGAAGATTGTT
1 AAGA-TTTTTCAAGTCCTATACTCCCTGAAAGAAGAGGGAGCAGACCCGTTTTTCGAAGATTGTT
* * * *
1427655 TGAGTCTTATACTCCCTGAAAGAAGAGGGAGCAGACCCTTTTTCCA
65 CGAGTCCTATACTCCCTGAAAGAAGAGGGAGCGGACCCGTTTT-CA
* ** *
1427701 AAAAAATTTCAAGTCTTATACTCCCTGAAAGAAGAGGGAGCAGACCCGTTTTTCGAAGATTGTTC
1 AAGATTTTTCAAGTCCTATACTCCCTGAAAGAAGAGGGAGCAGACCCGTTTTTCGAAGATTGTTC
* * * *
1427766 GAGTCCTATAATCCTTGAACGAAGATGGAGCGGACCCGTTCTTCA
66 GAGTCCTATACTCCCTGAAAGAAGAGGGAGCGGACCCGTT-TTCA
1427811 AAGATTTTTCAAGTC
1 AAGATTTTTCAAGTC
1427826 TCACTTATTC
Statistics
Matches: 187, Mismatches: 45, Indels: 8
0.78 0.19 0.03
Matches are distributed among these distances:
110 101 0.54
111 86 0.46
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (109 bp):
AAGATTTTTCAAGTCCTATACTCCCTGAAAGAAGAGGGAGCAGACCCGTTTTTCGAAGATTGTTC
GAGTCCTATACTCCCTGAAAGAAGAGGGAGCGGACCCGTTTTCA
Found at i:1430806 original size:21 final size:18
Alignment explanation
Indices: 1430766--1430809 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 18
1430756 TTCATTTAAG
*
1430766 AATTTTTTTTTAACTTTA
1 AATTTTTTTTTAACTATA
1430784 AATTTTTTTCTTAATCATATA
1 AATTTTTTT-TTAA-C-TATA
1430805 AATTT
1 AATTT
1430810 ATAAAATATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 9 0.41
19 4 0.18
20 1 0.05
21 8 0.36
ACGTcount: A:0.32, C:0.07, G:0.00, T:0.61
Consensus pattern (18 bp):
AATTTTTTTTTAACTATA
Found at i:1431367 original size:25 final size:24
Alignment explanation
Indices: 1431320--1431374 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 24
1431310 TATAACTGAT
*
1431320 TAAAAATTATTCTGTTTGCACCAC
1 TAAAAATTATTCTGCTTGCACCAC
*
1431344 TGAAAAATTATTAC-GCTTGTACCAC
1 T-AAAAATTATT-CTGCTTGCACCAC
1431369 TAAAAA
1 TAAAAA
1431375 CTATACTCGA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
24 6 0.22
25 20 0.74
26 1 0.04
ACGTcount: A:0.40, C:0.18, G:0.09, T:0.33
Consensus pattern (24 bp):
TAAAAATTATTCTGCTTGCACCAC
Found at i:1437140 original size:290 final size:291
Alignment explanation
Indices: 1436618--1437185 Score: 1066
Period size: 290 Copynumber: 2.0 Consensus size: 291
1436608 CCATTTGGAT
1436618 TCGCCTATAAATACCATTTTTTGTTTTTTTCTTCATTTTCATATGTACTCTCTCTACAAAAAAAA
1 TCGCCTATAAATACCATTTTTTGTTTTTTTCTTCATTTTCATATGTACTCTCTCTAC-AAAAAAA
1436683 ACTTTCCCTTCTCTCTAAGCCTCTCCAAAATCCGACGAGAGCTCAGCTGTTGGCAGCCACGCTAG
65 ACTTTCCCTTCTCTCTAAGCCTCTCCAAAATCCGACGAGAGCTCAGCTGTTGGCAGCCACGCTAG
* *
1436748 ACACCGTTGATTGCCATTTACGGTGACAGTTCGAGCCCAAATCTTTCAGGCTGGCTATTCTCGAC
130 ACACCGTTGATTGCCATTTACGGTGACAATTCGAGCCCAAATCTTTCAAGCTGGCTATTCTCGAC
1436813 GCGGGGAGTTTGGATCGAGGCTCCGATTTACGTGAAATGGTCTCCAACACTGTGAAAATGGTCGA
195 GCGGGGAGTTTGGATCGAGGCTCCGATTTACGTGAAATGGTCTCCAACACTGTGAAAATGGTCGA
1436878 GACTCTTCGGTTCTCCAAGGCTCTGATCGTCG
260 GACTCTTCGGTTCTCCAAGGCTCTGATCGTCG
1436910 TCGCCTATAAATACCATTTTTTGTTTTTTTCTTCATTTTCATATGTACTCTCTCTAC-AAAAAAA
1 TCGCCTATAAATACCATTTTTTGTTTTTTTCTTCATTTTCATATGTACTCTCTCTACAAAAAAAA
*
1436974 CTTTCCCTTCTCTCTAAGCCTCTCCAAAATCCGGCGAGAGCTCAGCTGTTGGCAGCCACGCTAGA
66 CTTTCCCTTCTCTCTAAGCCTCTCCAAAATCCGACGAGAGCTCAGCTGTTGGCAGCCACGCTAGA
*
1437039 CACCGTTGATTGCCGTTTACGGTGACAATTCGAGCCCAAATCTTTCAAGCTGGCTATTCTCGACG
131 CACCGTTGATTGCCATTTACGGTGACAATTCGAGCCCAAATCTTTCAAGCTGGCTATTCTCGACG
*
1437104 CGGGGAGTTTGGATCGAGGCTCTGATTTACGTGAAATGGTCTCCAACACTGTGAAAATGGTCGAG
196 CGGGGAGTTTGGATCGAGGCTCCGATTTACGTGAAATGGTCTCCAACACTGTGAAAATGGTCGAG
*
1437169 ACTCTTTGGTTCTCCAA
261 ACTCTTCGGTTCTCCAA
1437186 CACTATGAAA
Statistics
Matches: 270, Mismatches: 6, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
290 213 0.79
292 57 0.21
ACGTcount: A:0.23, C:0.26, G:0.20, T:0.32
Consensus pattern (291 bp):
TCGCCTATAAATACCATTTTTTGTTTTTTTCTTCATTTTCATATGTACTCTCTCTACAAAAAAAA
CTTTCCCTTCTCTCTAAGCCTCTCCAAAATCCGACGAGAGCTCAGCTGTTGGCAGCCACGCTAGA
CACCGTTGATTGCCATTTACGGTGACAATTCGAGCCCAAATCTTTCAAGCTGGCTATTCTCGACG
CGGGGAGTTTGGATCGAGGCTCCGATTTACGTGAAATGGTCTCCAACACTGTGAAAATGGTCGAG
ACTCTTCGGTTCTCCAAGGCTCTGATCGTCG
Found at i:1439691 original size:33 final size:34
Alignment explanation
Indices: 1439628--1439699 Score: 85
Period size: 35 Copynumber: 2.1 Consensus size: 34
1439618 AGTTGACAAC
*
1439628 AGAAAAAAAAAGAGAAAAGATATAGCAAAAAAAGA
1 AGAAAAAAAAAGAGAAAAGAGATA-CAAAAAAAGA
* *
1439663 AGAAAAAATAAGAGAAAGAGAGA-A-AAAAAAGGA
1 AGAAAAAAAAAGAGAAA-AGAGATACAAAAAAAGA
1439696 AGAA
1 AGAA
1439700 GAGAGAGAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
33 12 0.36
35 17 0.52
36 4 0.12
ACGTcount: A:0.74, C:0.01, G:0.21, T:0.04
Consensus pattern (34 bp):
AGAAAAAAAAAGAGAAAAGAGATACAAAAAAAGA
Found at i:1439702 original size:18 final size:19
Alignment explanation
Indices: 1439659--1439703 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
1439649 ATAGCAAAAA
*
1439659 AAGAAGA-AAAAATAAGAG
1 AAGAAGAGAAAAAAAAGAG
1439677 AA-AGAGAGAAAAAAAAG-G
1 AAGA-AGAGAAAAAAAAGAG
1439695 AAGAAGAGA
1 AAGAAGAGA
1439704 GAGAAATTGA
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
17 1 0.04
18 13 0.57
19 9 0.39
ACGTcount: A:0.71, C:0.00, G:0.27, T:0.02
Consensus pattern (19 bp):
AAGAAGAGAAAAAAAAGAG
Found at i:1439704 original size:22 final size:20
Alignment explanation
Indices: 1439658--1439709 Score: 63
Period size: 20 Copynumber: 2.5 Consensus size: 20
1439648 TATAGCAAAA
1439658 AAAGA-AGAAAAAATAAGAG
1 AAAGAGAGAAAAAATAAGAG
1439677 AAAGAGAGAAAAAA-AAGGAAG
1 AAAGAGAGAAAAAATAA-G-AG
1439698 AAGAGAGAGAAA
1 AA-AGAGAGAAA
1439710 TTGAAGCAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
19 7 0.24
20 9 0.31
21 4 0.14
22 9 0.31
ACGTcount: A:0.71, C:0.00, G:0.27, T:0.02
Consensus pattern (20 bp):
AAAGAGAGAAAAAATAAGAG
Found at i:1443526 original size:140 final size:141
Alignment explanation
Indices: 1443273--1443572 Score: 372
Period size: 140 Copynumber: 2.1 Consensus size: 141
1443263 CCAATAGAAA
* * * ** *
1443273 GGTTCGTAATGAGAAGGACTCATCTGATAGAGGGGAGAGAAAATTCATAATGAAAAGAACTTGTT
1 GGTTCATAATGAGAAGAACCCATCCAATAGAGGGGAGAGAAAATTCATAATGAAAAGAACTTATT
* * *
1443338 CAACCTTAGCTCGATTCATCGTATATGGAGTTGAATCAGCGACACCTCACTCGAGGGATCAACAT
66 CAACATTAGCTCGATTCATCGTATATGGAGTTAAATCAGCAACACCTCACTCGAGGGATCAACAT
* *
1443403 TTCCATTGGA-
131 TTCCAGTGCAG
* *
1443413 GGTTTATAATGAGAAGAACCCATCCAATAGAGGGGA-A-AATAAGTTCATAATGAGAAGAACTTA
1 GGTTCATAATGAGAAGAACCCATCCAATAGAGGGGAGAGAA-AA-TTCATAATGAAAAGAACTTA
** * * * * * *
1443476 TTCAACATTTTCTTGATTCATCGTATTTGGAGTTAAATCAGCAACTCCTCACTTGATGGATTAAC
64 TTCAACATTAGCTCGATTCATCGTATATGGAGTTAAATCAGCAACACCTCACTCGAGGGATCAAC
1443541 ATTTCCAGTGCAG
129 ATTTCCAGTGCAG
1443554 GGTTCATAATGAGAAGAAC
1 GGTTCATAATGAGAAGAAC
1443573 TAGTTCAACA
Statistics
Matches: 135, Mismatches: 22, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
138 2 0.01
139 3 0.02
140 112 0.83
141 18 0.13
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.28
Consensus pattern (141 bp):
GGTTCATAATGAGAAGAACCCATCCAATAGAGGGGAGAGAAAATTCATAATGAAAAGAACTTATT
CAACATTAGCTCGATTCATCGTATATGGAGTTAAATCAGCAACACCTCACTCGAGGGATCAACAT
TTCCAGTGCAG
Found at i:1443628 original size:100 final size:99
Alignment explanation
Indices: 1443454--1443673 Score: 314
Period size: 100 Copynumber: 2.2 Consensus size: 99
1443444 GGGGAAAATA
* * * *
1443454 AGTTCATAATGAGAAGAACTTATTCAACATTTTCTTGATTCATCGTATTTGGAGTTAAATCAGCA
1 AGTTCATAATGAGAAGAAC-TATTCAACATTTACTCGATTCATCATATATGGAGTTAAATCAGCA
* * *
1443519 ACTCCTCACTTGATGGATTAACATTTCCAGTGCAG
65 ACACCTCACTTGAGGGATTAACATTTCCAATGCAG
* * **
1443554 GGTTCATAATGAGAAGAACTAGTTCAACATTTACTCGATTCATCATATATGGAGTTGAATCAGTG
1 AGTTCATAATGAGAAGAACTA-TTCAACATTTACTCGATTCATCATATATGGAGTTAAATCAGCA
*
1443619 ACACCTCACTTGAGGGATTAACATTTCCAATGGAG
65 ACACCTCACTTGAGGGATTAACATTTCCAATGCAG
1443654 AGTTCATAATGAGAAGAACT
1 AGTTCATAATGAGAAGAACT
1443674 CGTCCGATAG
Statistics
Matches: 106, Mismatches: 13, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
99 2 0.02
100 104 0.98
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Consensus pattern (99 bp):
AGTTCATAATGAGAAGAACTATTCAACATTTACTCGATTCATCATATATGGAGTTAAATCAGCAA
CACCTCACTTGAGGGATTAACATTTCCAATGCAG
Found at i:1443749 original size:240 final size:240
Alignment explanation
Indices: 1443316--1443813 Score: 662
Period size: 240 Copynumber: 2.1 Consensus size: 240
1443306 GGAGAGAAAA
* *
1443316 TTCATAATGAAAAGAACTTGTTCAACCTTAGCTCGATTCATCGTATATGGAGTTGAATCAGCGAC
1 TTCATAATGAAAAGAACTAGTTCAACCTTAGCTCGATTCATCATATATGGAGTTGAATCAGCGAC
* *
1443381 ACCTCACTCGAGGGATCAACATTTCCATTGGAGGTTTATAATGAGAAGAACCCATCCAATAGAGG
66 ACCTCACTCGAGGGATCAACATTTCCAATGGAGGTTCATAATGAGAAGAACCCATCCAATAGAGG
** * * * *
1443446 GGAAAATAAGTTCATAATGAGAAGAACTTATTCAACATTTTCTTGATTCATCGTATTTGGAGTTA
131 GGAAAATAAGTTCATAACAAGAAGAACTTATTCAACATTTGCTCGATTCATCGCATATGGAGTTA
* * *
1443511 AATCAGCAACTCCTCACTTGATGGATTAACATTTCCAGTGCAGGG
196 AATCAGCAACGCCTCACTTGAGGGATTAACATTTCCAGTGCAGAG
* * *
1443556 TTCATAATGAGAAGAACTAGTTCAACATTTA-CTCGATTCATCATATATGGAGTTGAATCAGTGA
1 TTCATAATGAAAAGAACTAGTTCAAC-CTTAGCTCGATTCATCATATATGGAGTTGAATCAGCGA
* * * * *
1443620 CACCTCACTTGAGGGATTAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCGTCCGATAGA
65 CACCTCACTCGAGGGATCAACATTTCCAATGGAG-GTTCATAATGAGAAGAACCCATCCAATAGA
* *
1443685 -GGGAGAAA-AAGTTCATAACAAGAAGAACATT-TTTAACCTTTGCTCGATTCATCGCATATGGA
129 GGGGA-AAATAAGTTCATAACAAGAAGAAC-TTATTCAACATTTGCTCGATTCATCGCATATGGA
* * * * *
1443747 GTTGAATCAGTAACGCCTCACTTGAGGGCTTACCATTTCCAGTGGAGAG
192 GTTAAATCAGCAACGCCTCACTTGAGGGATTAACATTTCCAGTGCAGAG
* *
1443796 CTCATAATGAAAATAACT
1 TTCATAATGAAAAGAACT
1443814 CATCCGATGA
Statistics
Matches: 223, Mismatches: 31, Indels: 8
0.85 0.12 0.03
Matches are distributed among these distances:
240 189 0.85
241 34 0.15
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.29
Consensus pattern (240 bp):
TTCATAATGAAAAGAACTAGTTCAACCTTAGCTCGATTCATCATATATGGAGTTGAATCAGCGAC
ACCTCACTCGAGGGATCAACATTTCCAATGGAGGTTCATAATGAGAAGAACCCATCCAATAGAGG
GGAAAATAAGTTCATAACAAGAAGAACTTATTCAACATTTGCTCGATTCATCGCATATGGAGTTA
AATCAGCAACGCCTCACTTGAGGGATTAACATTTCCAGTGCAGAG
Found at i:1443907 original size:139 final size:140
Alignment explanation
Indices: 1443555--1443955 Score: 502
Period size: 139 Copynumber: 2.9 Consensus size: 140
1443545 CCAGTGCAGG
* * *
1443555 GTTCATAATGAGAAGAACTAGTTCAACATTTA-CTCGATTCATCATATATGGAGTTGAATCAGTG
1 GTTCATAATGAGAAGAACTTGTTCAAC-CTTAGCTCGATTCATCACATATGGAGTTGAATCAGTG
* * * * *
1443619 ACACCTCACTTGAGGGATTAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCGTCCGATAG
65 ACGCCTCACTTGAGGGATTAACATTTCCAGTGGAGAGCTCATAATGAAAAGAACTCATCCGATAG
*
1443684 AGGGAGAAAAA
130 AGAGAGAAAAA
** * * * *
1443695 GTTCATAACAAGAAGAACATT-TTTAACCTTTGCTCGATTCATCGCATATGGAGTTGAATCAGTA
1 GTTCATAATGAGAAGAAC-TTGTTCAACCTTAGCTCGATTCATCACATATGGAGTTGAATCAGTG
* * *
1443759 ACGCCTCACTTGAGGGCTTACCATTTCCAGTGGAGAGCTCATAATGAAAATAACTCATCCGAT-G
65 ACGCCTCACTTGAGGGATTAACATTTCCAGTGGAGAGCTCATAATGAAAAGAACTCATCCGATAG
*
1443823 AGAGAGAAGAA
130 AGAGAGAAAAA
* *
1443834 GTTCATAATGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCACATTTGGAGTTGAATCAGCGA
1 GTTCATAATGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCACATATGGAGTTGAATCAGTGA
* * * * * * **
1443899 TGCTTCACTCGAGGGATCAACATTTCCAGTAGAGAGCTCATAACGTGAAGAACTCAT
66 CGCCTCACTTGAGGGATTAACATTTCCAGTGGAGAGCTCATAATGAAAAGAACTCAT
1443956 GCTTGAAGAA
Statistics
Matches: 220, Mismatches: 38, Indels: 7
0.83 0.14 0.03
Matches are distributed among these distances:
138 2 0.01
139 112 0.51
140 105 0.48
141 1 0.00
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.27
Consensus pattern (140 bp):
GTTCATAATGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCACATATGGAGTTGAATCAGTGA
CGCCTCACTTGAGGGATTAACATTTCCAGTGGAGAGCTCATAATGAAAAGAACTCATCCGATAGA
GAGAGAAAAA
Found at i:1444136 original size:22 final size:22
Alignment explanation
Indices: 1444092--1444139 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
1444082 AAACATGCCT
*
1444092 CAAACTAGACCCGAACCATACC
1 CAAACTAGACCCGAACCAAACC
*
1444114 CAAACTAGACCC-CACCTAAACC
1 CAAACTAGACCCGAACC-AAACC
1444136 CAAA
1 CAAA
1444140 TTGTAACCTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 3 0.13
22 20 0.87
ACGTcount: A:0.44, C:0.42, G:0.06, T:0.08
Consensus pattern (22 bp):
CAAACTAGACCCGAACCAAACC
Done.