Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008374.1 Hibiscus syriacus cultivar Beakdansim tig00111131_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: 1731758
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 10
Found at i:1140851 original size:18 final size:18
Alignment explanation
Indices: 1140825--1140891 Score: 107
Period size: 18 Copynumber: 3.7 Consensus size: 18
1140815 TGCATTTTAT
*
1140825 GCATTGATGCACTTCCAC
1 GCATCGATGCACTTCCAC
*
1140843 GCATCGATGCACTTCCAT
1 GCATCGATGCACTTCCAC
1140861 GCATCGATGCACTTCCAC
1 GCATCGATGCACTTCCAC
*
1140879 ACATCGATGCACT
1 GCATCGATGCACT
1140892 CAGGATTTTA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 45 1.00
ACGTcount: A:0.24, C:0.34, G:0.16, T:0.25
Consensus pattern (18 bp):
GCATCGATGCACTTCCAC
Found at i:1140870 original size:36 final size:36
Alignment explanation
Indices: 1140823--1140891 Score: 120
Period size: 36 Copynumber: 1.9 Consensus size: 36
1140813 AATGCATTTT
* *
1140823 ATGCATTGATGCACTTCCACGCATCGATGCACTTCC
1 ATGCATCGATGCACTTCCACACATCGATGCACTTCC
1140859 ATGCATCGATGCACTTCCACACATCGATGCACT
1 ATGCATCGATGCACTTCCACACATCGATGCACT
1140892 CAGGATTTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.25, C:0.33, G:0.16, T:0.26
Consensus pattern (36 bp):
ATGCATCGATGCACTTCCACACATCGATGCACTTCC
Found at i:1140930 original size:46 final size:46
Alignment explanation
Indices: 1140880--1140982 Score: 147
Period size: 46 Copynumber: 2.2 Consensus size: 46
1140870 CACTTCCACA
1140880 CATCGATGCACT-CAGGATT-TTATGGAAAAATCGAATGCATTTTATG
1 CATCGATGCACTCCAGGATTGTT-T-GAAAAATCGAATGCATTTTATG
* * *
1140926 CATCGATGCACTCCAGGCTTGTTTGAAACATCGAATTCATTTTATG
1 CATCGATGCACTCCAGGATTGTTTGAAAAATCGAATGCATTTTATG
1140972 CATCGATGCAC
1 CATCGATGCAC
1140983 CCTTAGTGCA
Statistics
Matches: 52, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
46 43 0.83
47 7 0.13
48 2 0.04
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.32
Consensus pattern (46 bp):
CATCGATGCACTCCAGGATTGTTTGAAAAATCGAATGCATTTTATG
Found at i:1146525 original size:21 final size:21
Alignment explanation
Indices: 1146496--1146576 Score: 74
Period size: 21 Copynumber: 3.7 Consensus size: 21
1146486 TTTGTGCATA
1146496 ATGCATCGATACACTATGAAG
1 ATGCATCGATACACTATGAAG
* *
1146517 ATTCATCGATGCATCCCTATGAATG
1 ATGCATCGAT--A-CACTATGAA-G
*
1146542 -TGCATCGATACACCATGAAG
1 ATGCATCGATACACTATGAAG
* *
1146562 ATGCACCGATGCACT
1 ATGCATCGATACACT
1146577 CCTTGAATGT
Statistics
Matches: 47, Mismatches: 8, Indels: 10
0.72 0.12 0.15
Matches are distributed among these distances:
20 1 0.02
21 27 0.57
22 1 0.02
23 1 0.02
24 16 0.34
25 1 0.02
ACGTcount: A:0.32, C:0.25, G:0.19, T:0.25
Consensus pattern (21 bp):
ATGCATCGATACACTATGAAG
Found at i:1146561 original size:45 final size:44
Alignment explanation
Indices: 1146497--1146588 Score: 132
Period size: 45 Copynumber: 2.1 Consensus size: 44
1146487 TTGTGCATAA
* * *
1146497 TGCATCGATACACTATGAAGATTCATCGATGCA-TCCCTATGAATG
1 TGCATCGATACACCATGAAGATGCACCGATGCACT-CCT-TGAATG
1146542 TGCATCGATACACCATGAAGATGCACCGATGCACTCCTTGAATG
1 TGCATCGATACACCATGAAGATGCACCGATGCACTCCTTGAATG
1146586 TGC
1 TGC
1146589 GCACTCCTTG
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
44 9 0.21
45 33 0.77
46 1 0.02
ACGTcount: A:0.29, C:0.25, G:0.20, T:0.26
Consensus pattern (44 bp):
TGCATCGATACACCATGAAGATGCACCGATGCACTCCTTGAATG
Found at i:1146594 original size:17 final size:17
Alignment explanation
Indices: 1146572--1146605 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
1146562 ATGCACCGAT
1146572 GCACTCCTTGAATGTGC
1 GCACTCCTTGAATGTGC
1146589 GCACTCCTTGAATGTGC
1 GCACTCCTTGAATGTGC
1146606 ATCGATGCAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.18, C:0.29, G:0.24, T:0.29
Consensus pattern (17 bp):
GCACTCCTTGAATGTGC
Found at i:1149008 original size:45 final size:46
Alignment explanation
Indices: 1148954--1149056 Score: 149
Period size: 45 Copynumber: 2.3 Consensus size: 46
1148944 GCACTTCCAC
1148954 GCATCGATGCACT-CAGGATT-TTATGGAAACATCGAATGCA-TTTAT
1 GCATCGATGCACTCCAGGATTGTT-T-GAAACATCGAATGCATTTTAT
* *
1148999 GTATCGATGCACTCCAGGCTTGTTTGAAACATCGAATGCATTTTAT
1 GCATCGATGCACTCCAGGATTGTTTGAAACATCGAATGCATTTTAT
1149045 GCATCGATGCAC
1 GCATCGATGCAC
1149057 CCAAAACATG
Statistics
Matches: 52, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
45 27 0.52
46 23 0.44
47 2 0.04
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.31
Consensus pattern (46 bp):
GCATCGATGCACTCCAGGATTGTTTGAAACATCGAATGCATTTTAT
Found at i:1152625 original size:12 final size:12
Alignment explanation
Indices: 1152608--1152648 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
1152598 ATATTTATGA
1152608 AATTAAAAATAT
1 AATTAAAAATAT
1152620 AATTAAAAAT-T
1 AATTAAAAATAT
*
1152631 -ATTAAAATTAT
1 AATTAAAAATAT
*
1152642 ATTTAAA
1 AATTAAA
1152649 TTATGATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
10 8 0.32
11 2 0.08
12 15 0.60
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (12 bp):
AATTAAAAATAT
Found at i:1158759 original size:18 final size:18
Alignment explanation
Indices: 1158736--1158772 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
1158726 ATTATCAGTT
1158736 GTCCTTCGGGACATAGTG
1 GTCCTTCGGGACATAGTG
*
1158754 GTCCTTCGTGACATAGTG
1 GTCCTTCGGGACATAGTG
1158772 G
1 G
1158773 CTATTCGAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.16, C:0.22, G:0.32, T:0.30
Consensus pattern (18 bp):
GTCCTTCGGGACATAGTG
Found at i:1159045 original size:16 final size:16
Alignment explanation
Indices: 1159024--1159058 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
1159014 GTGTATGTTC
1159024 ATGATAATATTGTTAT
1 ATGATAATATTGTTAT
*
1159040 ATGATAATATTTTTAT
1 ATGATAATATTGTTAT
1159056 ATG
1 ATG
1159059 TTTATTTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.37, C:0.00, G:0.11, T:0.51
Consensus pattern (16 bp):
ATGATAATATTGTTAT
Found at i:1162589 original size:218 final size:219
Alignment explanation
Indices: 1162211--1162648 Score: 869
Period size: 218 Copynumber: 2.0 Consensus size: 219
1162201 GAAAAGTTAA
1162211 AGAAGATTTTAACAGAAGCTCCAGTGTTGGTTCAACCCAAGTCTGGCAAGAACTTCGTAGTGTAT
1 AGAAGATTTTAACAGAAGCTCCAGTGTTGGTTCAACCCAAGTCTGGCAAGAACTTCGTAGTGTAT
1162276 AGTGATGTGTTTCATAACGGTTTGGGATGCGTATTGATGCAAGAAGGTAAAGTGGTGGTTTATAC
66 AGTGATGTGTTTCATAACGGTTTGGGATGCGTATTGATGCAAGAAGGTAAAGTGGTGGTTTATAC
1162341 ATCGAGATAATTAAAACCGCACGAAAGAAATTATCCAACACACGATCTGGAGATGGCTGCAGTAG
131 ATCGAGATAATTAAAACCGCACGAAAGAAATTATCCAACACACGATCTGGAGATGGCTGCAGTAG
1162406 TGTTCGCTCTCAAGATCTGG-GTC
196 TGTTCGCTCTCAAGATCTGGCGTC
1162429 AGAAGATTTTAACAGAAGCTCCAGTGTTGGTTCAACCCAAGTCTGGCAAGAACTTCGTAGTGTAT
1 AGAAGATTTTAACAGAAGCTCCAGTGTTGGTTCAACCCAAGTCTGGCAAGAACTTCGTAGTGTAT
1162494 AGTGATGTGTTTCATAACGGTTTGGGATGCGTATTGATGCAAGAAGGTAAAGTGGTGGTTTATAC
66 AGTGATGTGTTTCATAACGGTTTGGGATGCGTATTGATGCAAGAAGGTAAAGTGGTGGTTTATAC
1162559 ATCGAGATAATTAAAACCGCACGAAAGAAATTATCCAACACACGATCTGGAGATGGCTGCAGTAG
131 ATCGAGATAATTAAAACCGCACGAAAGAAATTATCCAACACACGATCTGGAGATGGCTGCAGTAG
1162624 TGTTCGCTCTCAAGATCTGGCGTC
196 TGTTCGCTCTCAAGATCTGGCGTC
1162648 A
1 A
1162649 CTACTTGTAT
Statistics
Matches: 219, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
218 215 0.98
219 4 0.02
ACGTcount: A:0.30, C:0.17, G:0.26, T:0.27
Consensus pattern (219 bp):
AGAAGATTTTAACAGAAGCTCCAGTGTTGGTTCAACCCAAGTCTGGCAAGAACTTCGTAGTGTAT
AGTGATGTGTTTCATAACGGTTTGGGATGCGTATTGATGCAAGAAGGTAAAGTGGTGGTTTATAC
ATCGAGATAATTAAAACCGCACGAAAGAAATTATCCAACACACGATCTGGAGATGGCTGCAGTAG
TGTTCGCTCTCAAGATCTGGCGTC
Found at i:1168779 original size:2 final size:2
Alignment explanation
Indices: 1168772--1168806 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1168762 GCTAAAGTCC
1168772 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1168807 TAAATCCAGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1178056 original size:19 final size:20
Alignment explanation
Indices: 1178017--1178060 Score: 56
Period size: 22 Copynumber: 2.2 Consensus size: 20
1178007 ACAATTGAAT
1178017 TTGCCACGACATTTCATTCAA
1 TTGCCACGACA-TTCATTCAA
1178038 CTTGCCACGACA-T-ATTCAA
1 -TTGCCACGACATTCATTCAA
1178057 TTGC
1 TTGC
1178061 AACCATACTA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 4 0.18
19 6 0.27
20 1 0.05
22 11 0.50
ACGTcount: A:0.27, C:0.30, G:0.11, T:0.32
Consensus pattern (20 bp):
TTGCCACGACATTCATTCAA
Found at i:1178116 original size:22 final size:20
Alignment explanation
Indices: 1178076--1178116 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 20
1178066 TACTACCACC
*
1178076 ATTCCATTTTCACATCATTT
1 ATTCCATTTTCACAACATTT
1178096 ATTCCATTTTGCCACAACATT
1 ATTCCATTTT--CACAACATT
1178117 CTCATTTGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 10 0.56
22 8 0.44
ACGTcount: A:0.27, C:0.27, G:0.02, T:0.44
Consensus pattern (20 bp):
ATTCCATTTTCACAACATTT
Found at i:1180861 original size:20 final size:19
Alignment explanation
Indices: 1180819--1180883 Score: 76
Period size: 20 Copynumber: 3.3 Consensus size: 19
1180809 AAAATATTTT
* *
1180819 TATGAATAGTATTATATTG
1 TATGAATAGTATAATACTG
1180838 TATGAATAGTACTAATACTG
1 TATGAATAGTA-TAATACTG
*
1180858 TATGAATAGTATCGATACTG
1 TATGAATAGTAT-AATACTG
*
1180878 TGTGAA
1 TATGAA
1180884 CAGTTATGAC
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
19 12 0.30
20 28 0.70
ACGTcount: A:0.37, C:0.06, G:0.18, T:0.38
Consensus pattern (19 bp):
TATGAATAGTATAATACTG
Found at i:1183790 original size:17 final size:17
Alignment explanation
Indices: 1183760--1183816 Score: 55
Period size: 17 Copynumber: 3.4 Consensus size: 17
1183750 TTTGTTATTC
*
1183760 TTTG-TTAAAATTCAAT
1 TTTGTTTAAATTTCAAT
*
1183776 TTTGTTTAAGTTTCAAGT
1 TTTGTTTAAATTTCAA-T
* *
1183794 TTT-TTTAAATCTAAAT
1 TTTGTTTAAATTTCAAT
1183810 TTTGTTT
1 TTTGTTT
1183817 GGAATGCACT
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
16 8 0.24
17 21 0.64
18 4 0.12
ACGTcount: A:0.28, C:0.05, G:0.09, T:0.58
Consensus pattern (17 bp):
TTTGTTTAAATTTCAAT
Found at i:1184036 original size:18 final size:19
Alignment explanation
Indices: 1184015--1184071 Score: 71
Period size: 21 Copynumber: 2.9 Consensus size: 19
1184005 TATATTTTCC
1184015 AACAATTGGTAT-TTTTTT
1 AACAATTGGTATCTTTTTT
*
1184033 AACAATTGATATCCTTTTGTT
1 AACAATTGGTAT-CTTTT-TT
*
1184054 TACAATTGGTATCTTTTT
1 AACAATTGGTATCTTTTT
1184072 CATTAAACAT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
18 11 0.33
19 1 0.03
20 9 0.27
21 12 0.36
ACGTcount: A:0.26, C:0.11, G:0.11, T:0.53
Consensus pattern (19 bp):
AACAATTGGTATCTTTTTT
Found at i:1184320 original size:20 final size:20
Alignment explanation
Indices: 1184281--1184345 Score: 87
Period size: 20 Copynumber: 3.3 Consensus size: 20
1184271 AAAATATTTT
**
1184281 TATGAATAGTATTG-TACTG
1 TATGAATAGTACCGATACTG
1184300 TATGAATAGTACCGATACTG
1 TATGAATAGTACCGATACTG
*
1184320 TATGGATAGTACCGATACTG
1 TATGAATAGTACCGATACTG
*
1184340 TGTGAA
1 TATGAA
1184346 CATTTATGTA
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
19 12 0.30
20 28 0.70
ACGTcount: A:0.32, C:0.11, G:0.23, T:0.34
Consensus pattern (20 bp):
TATGAATAGTACCGATACTG
Found at i:1193184 original size:2 final size:2
Alignment explanation
Indices: 1193177--1193205 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1193167 ACCATATAAG
1193177 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1193206 CATTATAATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1194651 original size:27 final size:27
Alignment explanation
Indices: 1194621--1194680 Score: 111
Period size: 27 Copynumber: 2.2 Consensus size: 27
1194611 GTGTTATTAG
1194621 AAAATGTTCAAATTATGTATTTAGTTT
1 AAAATGTTCAAATTATGTATTTAGTTT
1194648 AAAATGTTCAAATTATGTATTTAGTTT
1 AAAATGTTCAAATTATGTATTTAGTTT
*
1194675 ACAATG
1 AAAATG
1194681 ATGGTTATAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.38, C:0.05, G:0.12, T:0.45
Consensus pattern (27 bp):
AAAATGTTCAAATTATGTATTTAGTTT
Found at i:1210019 original size:170 final size:171
Alignment explanation
Indices: 1209737--1210078 Score: 661
Period size: 170 Copynumber: 2.0 Consensus size: 171
1209727 CTTATTGCCA
1209737 ACACAAAGCCCTTACATTGCTTCTATAACACTAAGCGAACCTTTACCTTTTTAGCTTCTTATAAT
1 ACACAAAGCCCTTACATTGCTTCTATAACACTAAGCGAACCTTTACCTTTTTAGCTTCTTATAAT
1209802 ATTTAATAAGTCATCTTTGACATTACTTTAGTTTTATTTTCTTGCAA-TTTTTTAG-TTTTGTTT
66 ATTTAATAAGTCATCTTTGACATTACTTTAGTTTTATTTTCTTGCAATTTTTTTAGTTTTTGTTT
1209865 CTTTCAGTGCCGATTTTTTGCTACAACTATGTTTGCGACTTC
131 CTTTCAGTGCCGA-TTTTTGCTACAACTATGTTTGCGACTTC
1209907 ACACAAAGCCCTTACATTGCTTCTATAACACTAAGCGAACCTTTACCTTTTTAGCTTCTTATAAT
1 ACACAAAGCCCTTACATTGCTTCTATAACACTAAGCGAACCTTTACCTTTTTAGCTTCTTATAAT
1209972 ATTTAATAAGTCATCTTTGACATTACTTTAGTTTTATTTTCTTGCAATTTTTTTAGTTTTTGTTT
66 ATTTAATAAGTCATCTTTGACATTACTTTAGTTTTATTTTCTTGCAATTTTTTTAGTTTTTGTTT
1210037 CTTTCAGTGCCGATTTTTGCTACAACTATGTTTGCGACTTC
131 CTTTCAGTGCCGATTTTTGCTACAACTATGTTTGCGACTTC
1210078 A
1 A
1210079 ATGTTCTTCT
Statistics
Matches: 170, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
170 112 0.66
171 37 0.22
172 21 0.12
ACGTcount: A:0.24, C:0.19, G:0.11, T:0.46
Consensus pattern (171 bp):
ACACAAAGCCCTTACATTGCTTCTATAACACTAAGCGAACCTTTACCTTTTTAGCTTCTTATAAT
ATTTAATAAGTCATCTTTGACATTACTTTAGTTTTATTTTCTTGCAATTTTTTTAGTTTTTGTTT
CTTTCAGTGCCGATTTTTGCTACAACTATGTTTGCGACTTC
Found at i:1211848 original size:20 final size:20
Alignment explanation
Indices: 1211807--1211849 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
1211797 TTCCTACAGT
*
1211807 TTTTGAAACTATCTCTAGAG
1 TTTTGAAACTATCTCTAAAG
*
1211827 TTTTGAAACTTTCAT-TAAAG
1 TTTTGAAACTATC-TCTAAAG
1211847 TTT
1 TTT
1211850 CGATACTTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 19 0.95
21 1 0.05
ACGTcount: A:0.30, C:0.12, G:0.12, T:0.47
Consensus pattern (20 bp):
TTTTGAAACTATCTCTAAAG
Found at i:1214475 original size:44 final size:44
Alignment explanation
Indices: 1214425--1214515 Score: 139
Period size: 44 Copynumber: 2.1 Consensus size: 44
1214415 AAAAAACACA
* *
1214425 ATAGGAAATAAGTTCG-AAAAACTAGTAATATCTCCAACATAGTC
1 ATAGGAAATAAGTT-GAAAAAACTAGCAATAGCTCCAACATAGTC
*
1214469 ATAGGAAATAAGTTGAAAAAACTGGCAATAGCTCCAACATAGTC
1 ATAGGAAATAAGTTGAAAAAACTAGCAATAGCTCCAACATAGTC
1214513 ATA
1 ATA
1214516 TGAAGATTGT
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
43 1 0.02
44 42 0.98
ACGTcount: A:0.46, C:0.15, G:0.15, T:0.23
Consensus pattern (44 bp):
ATAGGAAATAAGTTGAAAAAACTAGCAATAGCTCCAACATAGTC
Found at i:1217860 original size:13 final size:13
Alignment explanation
Indices: 1217844--1217876 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
1217834 CATCTCCTTC
*
1217844 TTTCTTTCTTTAT
1 TTTCTTTCATTAT
1217857 TTTCTTTCATTAT
1 TTTCTTTCATTAT
1217870 TTTCTTT
1 TTTCTTT
1217877 TCACAATGCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.09, C:0.15, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTCTTTCATTAT
Found at i:1230740 original size:169 final size:171
Alignment explanation
Indices: 1230461--1230802 Score: 670
Period size: 169 Copynumber: 2.0 Consensus size: 171
1230451 CCGGAGAAAA
1230461 TTTGAAAAAAGGATTTGAATCTTCACTGGGCGATCCTACTTTGATGGTAACTCTATACGATCTAC
1 TTTGAAAAAAGGATTTGAATCTTCACTGGGCGATCCTACTTTGATGGTAACTCTATACGATCTAC
1230526 CATAGGAACCAAGAGTAATGAATTCTGGAACATCAAAAGGACTAGCAACTCTCATAAGAATTCTC
66 CATAGGAACCAAGAGTAATGAATTCTGGAACATCAAAAGGACTAGCAACTCTCATAAGAATTCTC
1230591 GCAGACGTGAGATCGT-CC-GTTCTTAGTGGACTCATGGAT
131 GCAGACGTGAGATCGTCCCTGTTCTTAGTGGACTCATGGAT
1230630 TTTGAAAAAAGGATTTGAATCTTCACTGGGCGATCCTACTTTGATGGTAACTCTATACGATCTAC
1 TTTGAAAAAAGGATTTGAATCTTCACTGGGCGATCCTACTTTGATGGTAACTCTATACGATCTAC
1230695 CATAGGAACCAAGAGTAATGAATTCTGGAACATCAAAAGGACTAGCAACTCTCATAAGAATTCTC
66 CATAGGAACCAAGAGTAATGAATTCTGGAACATCAAAAGGACTAGCAACTCTCATAAGAATTCTC
1230760 GCAGACGTGAGATCGTCCCTGTTCTTAGTGGACTCATGGAT
131 GCAGACGTGAGATCGTCCCTGTTCTTAGTGGACTCATGGAT
1230801 TT
1 TT
1230803 CTACCATATT
Statistics
Matches: 171, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
169 146 0.85
170 2 0.01
171 23 0.13
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.28
Consensus pattern (171 bp):
TTTGAAAAAAGGATTTGAATCTTCACTGGGCGATCCTACTTTGATGGTAACTCTATACGATCTAC
CATAGGAACCAAGAGTAATGAATTCTGGAACATCAAAAGGACTAGCAACTCTCATAAGAATTCTC
GCAGACGTGAGATCGTCCCTGTTCTTAGTGGACTCATGGAT
Found at i:1232171 original size:39 final size:40
Alignment explanation
Indices: 1232101--1232177 Score: 102
Period size: 39 Copynumber: 1.9 Consensus size: 40
1232091 GTCCTCAAAC
* *
1232101 ATTTCATTCTTTTCTCTTTAAGACTCCACCTCTGCCTCAA
1 ATTTCATTCTTTTCTCTCTAAGACTCCACCTCAGCCTCAA
* **
1232141 ATTT-ATTCTTTTCTCTCTCAGACTGTACCTCAGCCTC
1 ATTTCATTCTTTTCTCTCTAAGACTCCACCTCAGCCTC
1232178 TTTCTCAGTC
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
39 28 0.88
40 4 0.12
ACGTcount: A:0.18, C:0.32, G:0.06, T:0.43
Consensus pattern (40 bp):
ATTTCATTCTTTTCTCTCTAAGACTCCACCTCAGCCTCAA
Found at i:1234038 original size:101 final size:101
Alignment explanation
Indices: 1233863--1234066 Score: 408
Period size: 101 Copynumber: 2.0 Consensus size: 101
1233853 GTTTGTGCAA
1233863 AGATGCTTAAGGACTGAGGGCTTTAATATCAAGGTGGTAAGGTGGGGTTTTGCGAAAAATGCTTG
1 AGATGCTTAAGGACTGAGGGCTTTAATATCAAGGTGGTAAGGTGGGGTTTTGCGAAAAATGCTTG
1233928 TCTGATTGTCTTTCAGTCTGTGGAAGAGAAAAACAC
66 TCTGATTGTCTTTCAGTCTGTGGAAGAGAAAAACAC
1233964 AGATGCTTAAGGACTGAGGGCTTTAATATCAAGGTGGTAAGGTGGGGTTTTGCGAAAAATGCTTG
1 AGATGCTTAAGGACTGAGGGCTTTAATATCAAGGTGGTAAGGTGGGGTTTTGCGAAAAATGCTTG
1234029 TCTGATTGTCTTTCAGTCTGTGGAAGAGAAAAACAC
66 TCTGATTGTCTTTCAGTCTGTGGAAGAGAAAAACAC
1234065 AG
1 AG
1234067 CGGTGGAGGA
Statistics
Matches: 103, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
101 103 1.00
ACGTcount: A:0.29, C:0.12, G:0.30, T:0.29
Consensus pattern (101 bp):
AGATGCTTAAGGACTGAGGGCTTTAATATCAAGGTGGTAAGGTGGGGTTTTGCGAAAAATGCTTG
TCTGATTGTCTTTCAGTCTGTGGAAGAGAAAAACAC
Found at i:1237621 original size:19 final size:19
Alignment explanation
Indices: 1237597--1237635 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
1237587 TTTCTTATTC
1237597 CTTTCTTTTCTATGTTTTG
1 CTTTCTTTTCTATGTTTTG
1237616 CTTTCTTTTCTATGTTTTG
1 CTTTCTTTTCTATGTTTTG
1237635 C
1 C
1237636 ATTTTCTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.05, C:0.18, G:0.10, T:0.67
Consensus pattern (19 bp):
CTTTCTTTTCTATGTTTTG
Found at i:1244209 original size:27 final size:27
Alignment explanation
Indices: 1244179--1244232 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
1244169 GAACAATTTT
*
1244179 TTTACATCTTATACAAAGACATGAGGA
1 TTTACATCTTACACAAAGACATGAGGA
1244206 TTTACATCTTACACAAAGACATGAGGA
1 TTTACATCTTACACAAAGACATGAGGA
1244233 ATCTAAGACA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.41, C:0.17, G:0.15, T:0.28
Consensus pattern (27 bp):
TTTACATCTTACACAAAGACATGAGGA
Found at i:1246222 original size:21 final size:21
Alignment explanation
Indices: 1246192--1246232 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1246182 CCAGAAATTA
* *
1246192 GATAACAAAATTAACATTTTT
1 GATAAAAAAAATAACATTTTT
*
1246213 GATAAAAAAAATAATATTTT
1 GATAAAAAAAATAACATTTT
1246233 AAGTAACATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.54, C:0.05, G:0.05, T:0.37
Consensus pattern (21 bp):
GATAAAAAAAATAACATTTTT
Found at i:1257821 original size:20 final size:20
Alignment explanation
Indices: 1257796--1257847 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
1257786 TCTCTACTTA
* *
1257796 TAGTATCGATACCT-TATCTT
1 TAGTATCGATACCTCCA-CAT
1257816 TAGTATCGATACCTCCACAT
1 TAGTATCGATACCTCCACAT
1257836 TAGTATCGATAC
1 TAGTATCGATAC
1257848 TACTTCAATC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 28 0.97
21 1 0.03
ACGTcount: A:0.29, C:0.23, G:0.12, T:0.37
Consensus pattern (20 bp):
TAGTATCGATACCTCCACAT
Found at i:1259021 original size:23 final size:23
Alignment explanation
Indices: 1258946--1259054 Score: 111
Period size: 23 Copynumber: 4.9 Consensus size: 23
1258936 AGCTCGTAAT
*
1258946 TTGCACCGAAGTGCCATATA--A
1 TTGCACCGAAGTGCCATATAGGG
* *
1258967 TTGTC-CCGAAG-GACCACATA-GT
1 TTG-CACCGAAGTG-CCATATAGGG
*
1258989 TTGCACCGAAGTGTCATATAGGG
1 TTGCACCGAAGTGCCATATAGGG
*
1259012 TTGCATCGAAGTGCCATATAGGG
1 TTGCACCGAAGTGCCATATAGGG
*
1259035 TTGTACCGAAGTGCCATATA
1 TTGCACCGAAGTGCCATATA
1259055 TTTTTCCTAG
Statistics
Matches: 73, Mismatches: 9, Indels: 10
0.79 0.10 0.11
Matches are distributed among these distances:
20 1 0.01
21 16 0.22
22 15 0.21
23 41 0.56
ACGTcount: A:0.28, C:0.21, G:0.25, T:0.26
Consensus pattern (23 bp):
TTGCACCGAAGTGCCATATAGGG
Found at i:1266735 original size:20 final size:20
Alignment explanation
Indices: 1266690--1266741 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
1266680 ATGTTTTAAG
*
1266690 GGTATCGATACCATCCTACA
1 GGTATCGATACCACCCTACA
* *
1266710 GATATCGATACTACCCTTAC-
1 GGTATCGATACCACCC-TACA
1266730 GGTATCGATACC
1 GGTATCGATACC
1266742 TCTATCAACA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
20 23 0.88
21 3 0.12
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.27
Consensus pattern (20 bp):
GGTATCGATACCACCCTACA
Found at i:1269207 original size:41 final size:39
Alignment explanation
Indices: 1269140--1269222 Score: 96
Period size: 40 Copynumber: 2.1 Consensus size: 39
1269130 GATGCTAAAT
* *
1269140 AATAAAATAAATATTAAATAAGTAAAATGGAAAAAGAAAAA
1 AATAAAATAAATA-TAAAAAAGTAAAAT-CAAAAAGAAAAA
*
1269181 AATAATAATAAATA-AAAAAAGATAAAATCAAAAGGAAAAA
1 AATAA-AATAAATATAAAAAAG-TAAAATCAAAAAGAAAAA
1269221 AA
1 AA
1269223 GAGAACAAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
40 18 0.49
41 11 0.30
42 8 0.22
ACGTcount: A:0.73, C:0.01, G:0.08, T:0.17
Consensus pattern (39 bp):
AATAAAATAAATATAAAAAAGTAAAATCAAAAAGAAAAA
Found at i:1271862 original size:37 final size:39
Alignment explanation
Indices: 1271804--1271877 Score: 109
Period size: 37 Copynumber: 1.9 Consensus size: 39
1271794 GTAAAAGGGG
*
1271804 AAAAGGGAAAAATAATAAATAAAAAAAAAGAT-AAAATC
1 AAAAGGGAAAAATAAGAAATAAAAAAAAAGATCAAAATC
1271842 AAAA-GGAAAAA-AAGAGAATAAAAAAAAAGATCAAAA
1 AAAAGGGAAAAATAAGA-AATAAAAAAAAAGATCAAAA
1271878 GGAAAAAATA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
36 3 0.09
37 22 0.67
38 8 0.24
ACGTcount: A:0.76, C:0.03, G:0.12, T:0.09
Consensus pattern (39 bp):
AAAAGGGAAAAATAAGAAATAAAAAAAAAGATCAAAATC
Found at i:1271869 original size:24 final size:24
Alignment explanation
Indices: 1271824--1271870 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
1271814 AATAATAAAT
*
1271824 AAAAAAAAAGATAAAATCAAAAGG
1 AAAAAAAAAGATAAAATAAAAAGG
*
1271848 AAAAAAAGAGAATAAAA-AAAAAG
1 AAAAAAAAAG-ATAAAATAAAAAG
1271871 ATCAAAAGGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.79, C:0.02, G:0.13, T:0.06
Consensus pattern (24 bp):
AAAAAAAAAGATAAAATAAAAAGG
Found at i:1272007 original size:28 final size:25
Alignment explanation
Indices: 1271976--1272062 Score: 86
Period size: 28 Copynumber: 3.2 Consensus size: 25
1271966 TGAAATTGAG
*
1271976 TAAAAATACTAATAAAGAAATAAAAGAA
1 TAAAAAAAC-AATAAA-AAATAAAA-AA
*
1272004 TAAAAAAAC-ATAAAAAATAATAAA
1 TAAAAAAACAATAAAAAATAAAAAA
1272028 TAAAAAAACAAAGTAGAAAAATAAAATAA
1 TAAAAAAAC-AA-TA-AAAAATAAAA-AA
1272057 TAAAAA
1 TAAAAA
1272063 GGGTTAAATT
Statistics
Matches: 51, Mismatches: 3, Indels: 9
0.81 0.05 0.14
Matches are distributed among these distances:
24 11 0.22
25 7 0.14
26 6 0.12
27 2 0.04
28 17 0.33
29 8 0.16
ACGTcount: A:0.76, C:0.03, G:0.05, T:0.16
Consensus pattern (25 bp):
TAAAAAAACAATAAAAAATAAAAAA
Found at i:1272031 original size:24 final size:26
Alignment explanation
Indices: 1271987--1272037 Score: 79
Period size: 24 Copynumber: 2.0 Consensus size: 26
1271977 AAAAATACTA
1271987 ATAAAGAAATAAAAGAATAAAAAAAC
1 ATAAAGAAATAAAAGAATAAAAAAAC
*
1272013 ATAAA-AAATAATA-AATAAAAAAAC
1 ATAAAGAAATAAAAGAATAAAAAAAC
1272037 A
1 A
1272038 AAGTAGAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 12 0.50
25 7 0.29
26 5 0.21
ACGTcount: A:0.78, C:0.04, G:0.04, T:0.14
Consensus pattern (26 bp):
ATAAAGAAATAAAAGAATAAAAAAAC
Found at i:1273648 original size:81 final size:79
Alignment explanation
Indices: 1273549--1273838 Score: 303
Period size: 81 Copynumber: 3.6 Consensus size: 79
1273539 CTATATTGTG
* *
1273549 AATGATGTGCCTTGAGCTGAGTGGAATCAAACTCGAAGGTCTTTGGCAGATAACCCTTTTAGCCT
1 AATGATGTGCCTTGAGCTGAGTGGAATCGAACTCAAAGGTCTTTGGCAGATAACCCTTTTAGCCT
*
1273614 TGAGCTACGCTGCA
66 TGAGCTATGCTGCA
* *
1273628 AATGATAGTGCCTTTGAGCTGAGTGGAATCGAACTCTAAGGTTTTTGGCAGATAACCCTTCTT-G
1 AATGAT-GTGCC-TTGAGCTGAGTGGAATCGAACTCAAAGGTCTTTGGCAGATAACCCTT-TTAG
* * *
1273692 CCTTAAGCTATACTACA
63 CCTTGAGCTATGCTGCA
* * * * * * * *
1273709 AATGATATGTCGTTGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTATCGACAGATAACCATTCTA
1 AATGATGTG-CCTTGAGCTGAGTGGAATCGAACTCAAAGGTC-TT-T-GGCAGATAACCCTTTTA
* *
1273774 GCCTTGAGTTATGTTGCA
62 GCCTTGAGCTATGCTGCA
* * *
1273792 AATGATGTGCCCTCGAAGCTGAGTGTAGTCGAACTCAAAGGTCTTTG
1 AATGATGTG-CCTTG-AGCTGAGTGGAATCGAACTCAAAGGTCTTTG
1273839 TGTTTCATAA
Statistics
Matches: 175, Mismatches: 27, Indels: 16
0.80 0.12 0.07
Matches are distributed among these distances:
79 6 0.03
80 32 0.18
81 68 0.39
82 5 0.03
83 38 0.22
84 26 0.15
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.30
Consensus pattern (79 bp):
AATGATGTGCCTTGAGCTGAGTGGAATCGAACTCAAAGGTCTTTGGCAGATAACCCTTTTAGCCT
TGAGCTATGCTGCA
Found at i:1273955 original size:34 final size:33
Alignment explanation
Indices: 1273853--1273972 Score: 190
Period size: 33 Copynumber: 3.7 Consensus size: 33
1273843 TCATAAGGGT
1273853 TTTTTTGTGTTT-AA-AGAAACGATTTCAAAGG
1 TTTTTTGTGTTTCAAGAGAAACGATTTCAAAGG
*
1273884 TTTTTTGTATTTCAAGAGAAACGATTTCAAAGG
1 TTTTTTGTGTTTCAAGAGAAACGATTTCAAAGG
*
1273917 TTTTTTGTGTTTCAAGAGAAACGCTTTCAAAGG
1 TTTTTTGTGTTTCAAGAGAAACGATTTCAAAGG
*
1273950 TTTTTTTTTGTTTCAAGAGAAAC
1 -TTTTTTGTGTTTCAAGAGAAAC
1273973 TGTATCTAGG
Statistics
Matches: 82, Mismatches: 4, Indels: 3
0.92 0.04 0.03
Matches are distributed among these distances:
31 11 0.13
32 2 0.02
33 48 0.59
34 21 0.26
ACGTcount: A:0.30, C:0.09, G:0.18, T:0.42
Consensus pattern (33 bp):
TTTTTTGTGTTTCAAGAGAAACGATTTCAAAGG
Found at i:1274058 original size:67 final size:67
Alignment explanation
Indices: 1273958--1274084 Score: 168
Period size: 67 Copynumber: 1.9 Consensus size: 67
1273948 GGTTTTTTTT
* * *
1273958 TGTTTCAAGAGAAACTGTATCTAGGGAGGCAAAA-TTATCTTTCAAGAGAAACATAT-TCAAAGG
1 TGTTTCAAGAGAAACTGTATCAAGAGAGACAAAACTT-TCTTTCAAGAGAAAC-TATCTCAAAGG
1274021 TTGG
64 TTGG
* * *
1274025 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACTATCTCAA
1 TGTTTCAAGAGAAACTGTATCAAGAGAGACAAAACTTTCTTTCAAGAGAAACTATCTCAA
1274085 GAGAAACAAA
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
66 3 0.06
67 47 0.90
68 2 0.04
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.28
Consensus pattern (67 bp):
TGTTTCAAGAGAAACTGTATCAAGAGAGACAAAACTTTCTTTCAAGAGAAACTATCTCAAAGGTT
GG
Found at i:1274117 original size:73 final size:72
Alignment explanation
Indices: 1274025--1274312 Score: 335
Period size: 73 Copynumber: 4.1 Consensus size: 72
1274015 CAAAGGTTGG
* * * *
1274025 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACTATCTCAAGAGAA
1 TGTTTCAAGAGAAAATGTCTCAAGAGAGACAAAA-TTTGTTTCAAGAGAAACTGTCTCAAGAGAG
1274090 ACAAAATT
65 ACAAAATT
* * *
1274098 TGTTTCAAGAGAAAATGTCTCAAGAGAGACAAAACTTTGTTCCAAAAGAAACTGTCTCAAGGGAG
1 TGTTTCAAGAGAAAATGTCTCAAGAGAGACAAAA-TTTGTTTCAAGAGAAACTGTCTCAAGAGAG
*
1274163 ACGAAATT
65 ACAAAATT
* * * *
1274171 TGTTTCAAG-GAAAACATAT-TC---AGAG-----ATTTTTTTCAAGGGAAACTGTCTCAAAAGA
1 TGTTTCAAGAG-AAA-ATGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGA
1274226 GACAAAATT
64 GACAAAATT
* *
1274235 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGA
1 TGTTTCAAGAGAAAATGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGA
1274300 CAAAACTT
66 CAAAA-TT
1274308 TGTTT
1 TGTTT
1274313 TGAGTAAATT
Statistics
Matches: 181, Mismatches: 21, Indels: 26
0.79 0.09 0.11
Matches are distributed among these distances:
63 2 0.01
64 45 0.25
65 2 0.01
67 4 0.02
70 4 0.02
72 35 0.19
73 86 0.48
74 3 0.02
ACGTcount: A:0.40, C:0.14, G:0.19, T:0.26
Consensus pattern (72 bp):
TGTTTCAAGAGAAAATGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGA
CAAAATT
Found at i:1274119 original size:36 final size:36
Alignment explanation
Indices: 1274025--1274312 Score: 344
Period size: 36 Copynumber: 8.1 Consensus size: 36
1274015 CAAAGGTTGG
1274025 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TT
* * *
1274062 TGTTTCAAGGGAAACTATCTCAAGAGAAACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
*
1274098 TGTTTCAAGAGAAAATGTCTCAAGAGAGACAAAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TT
* * * *
1274135 TGTTCCAAAAGAAACTGTCTCAAGGGAGACGAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
*
1274171 TGTTTCAAG-GAAAACATAT-TC---AGAG-----ATT
1 TGTTTCAAGAG-AAAC-TGTCTCAAGAGAGACAAAATT
* * *
1274199 TTTTTCAAGGGAAACTGTCTCAAAAGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
*
1274235 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
1274271 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TT
1274308 TGTTT
1 TGTTT
1274313 TGAGTAAATT
Statistics
Matches: 216, Mismatches: 21, Indels: 28
0.82 0.08 0.11
Matches are distributed among these distances:
27 2 0.01
28 17 0.08
29 1 0.00
31 4 0.02
33 3 0.01
35 1 0.00
36 117 0.54
37 71 0.33
ACGTcount: A:0.40, C:0.14, G:0.19, T:0.26
Consensus pattern (36 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
Found at i:1274233 original size:137 final size:137
Alignment explanation
Indices: 1274064--1274312 Score: 401
Period size: 137 Copynumber: 1.8 Consensus size: 137
1274054 CAAAACTTTG
*
1274064 TTTCAAGGGAAACTATCTCAAGAGAAACAAAATTTGTTTCAAGAGAAAATGTCTCAAGAGAGACA
1 TTTCAAGGGAAACTATCTCAAAAGAAACAAAATTTGTTTCAAGAGAAAATGTCTCAAGAGAGACA
* *
1274129 AAACTTTGTTCCAAAAGAAACTGTCTCAAGGGAGACGAAA-TTTGTTTCAAGGAAAACATATTCA
66 AAA-TTTGTTCCAAAAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGAAAACATATTCA
1274193 GAGATTTT
130 GAGATTTT
* * * *
1274201 TTTCAAGGGAAACTGTCTCAAAAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACA
1 TTTCAAGGGAAACTATCTCAAAAGAAACAAAATTTGTTTCAAGAGAAAATGTCTCAAGAGAGACA
* *
1274266 AAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTT
66 AAATTTGTTCCAAAAGAAACTGTCTCAAGAGAGACAAAACTTTGTTT
1274313 TGAGTAAATT
Statistics
Matches: 102, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
136 32 0.31
137 70 0.69
ACGTcount: A:0.41, C:0.14, G:0.19, T:0.27
Consensus pattern (137 bp):
TTTCAAGGGAAACTATCTCAAAAGAAACAAAATTTGTTTCAAGAGAAAATGTCTCAAGAGAGACA
AAATTTGTTCCAAAAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGAAAACATATTCAG
AGATTTT
Found at i:1274264 original size:100 final size:102
Alignment explanation
Indices: 1274095--1274284 Score: 285
Period size: 100 Copynumber: 1.9 Consensus size: 102
1274085 GAGAAACAAA
* *
1274095 ATTTGTTTCAAGAGAAAATGTCTCAAGAGAGACAAAACTTTGTTCCAAAAGAAACTGTCTCAAGG
1 ATTTGTTTCAAGAGAAAATGTCTCAAAAGAGACAAAACTTTGTTCCAAAAGAAACTGTCTCAAGA
*
1274160 GAGACGAAATTTGTTTCAAG-GAAAACATATTCAGAG
66 GAGACAAAATTTGTTTCAAGAGAAAACATATTCAGAG
* * * * **
1274196 ATTTTTTTCAAGGGAAACTGTCTCAAAAGAGACAAAA-TTTGTTTCAAGGGAAACTGTCTCAAGA
1 ATTTGTTTCAAGAGAAAATGTCTCAAAAGAGACAAAACTTTGTTCCAAAAGAAACTGTCTCAAGA
1274260 GAGACAAAATTTGTTTCAAGAGAAA
66 GAGACAAAATTTGTTTCAAGAGAAA
1274285 CTGTCTCAAG
Statistics
Matches: 79, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
100 42 0.53
101 37 0.47
ACGTcount: A:0.41, C:0.13, G:0.19, T:0.27
Consensus pattern (102 bp):
ATTTGTTTCAAGAGAAAATGTCTCAAAAGAGACAAAACTTTGTTCCAAAAGAAACTGTCTCAAGA
GAGACAAAATTTGTTTCAAGAGAAAACATATTCAGAG
Found at i:1274278 original size:173 final size:176
Alignment explanation
Indices: 1273956--1274311 Score: 531
Period size: 173 Copynumber: 2.0 Consensus size: 176
1273946 AAGGTTTTTT
* * * * *
1273956 TTTGTTTCAAGAGAAACTGTATCTAGGGAGGCAAAATTATCTTTCAAGAGAAACATATTCAAAGG
1 TTTGTTCCAAAAGAAACTGTATCAAGGGAGACAAAATTATCTTTCAAGAGAAACATATTCAAAGA
*
1274021 TTGGTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACTATCTCAAG
66 TT-GTGTTTCAAGAGAAACTGTCTCAAAAGAGACAAAACTTTGTTTCAAGGGAAACTATCTCAAG
1274086 AGAAACAAAATTTGTTTCAAGAGAAAATGTCTCAAGAGAGACAAAAC
130 AGAAACAAAATTTGTTTCAAGAGAAAATGTCTCAAGAGAGACAAAAC
* * * *
1274133 TTTGTTCCAAAAGAAACTGTCTCAAGGGAGACGAAATT-TGTTTCAAG-GAAAACATATTCAGAG
1 TTTGTTCCAAAAGAAACTGTATCAAGGGAGACAAAATTATCTTTCAAGAG-AAACATATTCAAAG
* * *
1274196 ATT-TTTTTCAAGGGAAACTGTCTCAAAAGAGACAAAA-TTTGTTTCAAGGGAAACTGTCTCAAG
65 ATTGTGTTTCAAGAGAAACTGTCTCAAAAGAGACAAAACTTTGTTTCAAGGGAAACTATCTCAAG
* *
1274259 AGAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAAC
130 AGAAACAAAATTTGTTTCAAGAGAAAATGTCTCAAGAGAGACAAAAC
1274306 TTTGTT
1 TTTGTT
1274312 TTGAGTAAAT
Statistics
Matches: 163, Mismatches: 15, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
173 76 0.47
174 31 0.19
175 1 0.01
176 23 0.14
177 32 0.20
ACGTcount: A:0.40, C:0.14, G:0.20, T:0.27
Consensus pattern (176 bp):
TTTGTTCCAAAAGAAACTGTATCAAGGGAGACAAAATTATCTTTCAAGAGAAACATATTCAAAGA
TTGTGTTTCAAGAGAAACTGTCTCAAAAGAGACAAAACTTTGTTTCAAGGGAAACTATCTCAAGA
GAAACAAAATTTGTTTCAAGAGAAAATGTCTCAAGAGAGACAAAAC
Found at i:1274280 original size:21 final size:21
Alignment explanation
Indices: 1274218--1274282 Score: 61
Period size: 21 Copynumber: 3.4 Consensus size: 21
1274208 GGAAACTGTC
*
1274218 TCAAAAGAGACAAAATTTGTT
1 TCAAGAGAGACAAAATTTGTT
* *
1274239 TCAAG-G-G---AAA-CTGTC
1 TCAAGAGAGACAAAATTTGTT
1274254 TCAAGAGAGACAAAATTTGTT
1 TCAAGAGAGACAAAATTTGTT
1274275 TCAAGAGA
1 TCAAGAGA
1274283 AACTGTCTCA
Statistics
Matches: 33, Mismatches: 5, Indels: 12
0.66 0.10 0.24
Matches are distributed among these distances:
15 8 0.24
16 4 0.12
17 1 0.03
19 1 0.03
20 4 0.12
21 15 0.45
ACGTcount: A:0.43, C:0.12, G:0.20, T:0.25
Consensus pattern (21 bp):
TCAAGAGAGACAAAATTTGTT
Found at i:1275519 original size:12 final size:12
Alignment explanation
Indices: 1275502--1275588 Score: 99
Period size: 12 Copynumber: 7.3 Consensus size: 12
1275492 CATATGTGTC
1275502 TTCTTTTCTTTT
1 TTCTTTTCTTTT
*
1275514 TTCTTTATTTTCTT
1 TTCTTT-TCTT-TT
* **
1275528 TTGTTTT-TGCT
1 TTCTTTTCTTTT
1275539 TT-TTTTCTTTT
1 TTCTTTTCTTTT
1275550 TTCTTTTCTTTT
1 TTCTTTTCTTTT
1275562 TTCTTTTCTTTT
1 TTCTTTTCTTTT
1275574 TTCTTTT-TTTT
1 TTCTTTTCTTTT
1275585 TTCT
1 TTCT
1275589 CTTTTTTCTG
Statistics
Matches: 65, Mismatches: 6, Indels: 9
0.81 0.08 0.11
Matches are distributed among these distances:
10 4 0.06
11 15 0.23
12 35 0.54
13 4 0.06
14 7 0.11
ACGTcount: A:0.01, C:0.14, G:0.02, T:0.83
Consensus pattern (12 bp):
TTCTTTTCTTTT
Found at i:1275573 original size:32 final size:32
Alignment explanation
Indices: 1275502--1275615 Score: 108
Period size: 32 Copynumber: 3.4 Consensus size: 32
1275492 CATATGTGTC
1275502 TTCTTTTCTTT-TTTCTTTATTTTCTTTTGTT-TT
1 TTCTTTT-TTTCTTT-TTTATTTTCTTTT-TTCTT
* *
1275535 TGCTTTTTTTCTTTTTTCTTTTCTTTTTTCTT
1 TTCTTTTTTTCTTTTTTATTTTCTTTTTTCTT
*
1275567 TTC-TTTTTTCTTTTTTTTTTCTCTTTTTTCTGCT
1 TTCTTTTTTTCTTTTTTATTT-TCTTTTTTCT--T
1275601 TCTCTTTTTATTCTT
1 T-TCTTTTT-TTCTT
1275616 GATTGGATCT
Statistics
Matches: 69, Mismatches: 4, Indels: 12
0.81 0.05 0.14
Matches are distributed among these distances:
31 18 0.26
32 29 0.42
33 9 0.13
34 2 0.03
35 2 0.03
36 4 0.06
37 5 0.07
ACGTcount: A:0.02, C:0.16, G:0.03, T:0.80
Consensus pattern (32 bp):
TTCTTTTTTTCTTTTTTATTTTCTTTTTTCTT
Found at i:1275591 original size:20 final size:20
Alignment explanation
Indices: 1275502--1275597 Score: 126
Period size: 20 Copynumber: 4.8 Consensus size: 20
1275492 CATATGTGTC
1275502 TTCTTTTCTTTTTTCTTTATT
1 TTCTTTTCTTTTTTCTTT-TT
* *
1275523 TTCTTTTGTTTTTGCTTTTT
1 TTCTTTTCTTTTTTCTTTTT
1275543 TTCTTTT-TTCTTTTC-TTTT
1 TTCTTTTCTT-TTTTCTTTTT
1275562 TTCTTTTCTTTTTTCTTTTT
1 TTCTTTTCTTTTTTCTTTTT
1275582 TT-TTTCTCTTTTTTCT
1 TTCTTT-TCTTTTTTCT
1275598 GCTTCTCTTT
Statistics
Matches: 68, Mismatches: 3, Indels: 9
0.85 0.04 0.11
Matches are distributed among these distances:
19 21 0.31
20 31 0.46
21 16 0.24
ACGTcount: A:0.01, C:0.15, G:0.02, T:0.82
Consensus pattern (20 bp):
TTCTTTTCTTTTTTCTTTTT
Found at i:1275593 original size:12 final size:12
Alignment explanation
Indices: 1275503--1275609 Score: 62
Period size: 12 Copynumber: 8.6 Consensus size: 12
1275493 ATATGTGTCT
1275503 TCTTTTCTTTTT-
1 TCTTTT-TTTTTC
*
1275515 TC-TTTATTTTC
1 TCTTTTTTTTTC
*
1275526 T-TTTGTTTTTGC
1 TCTTT-TTTTTTC
* *
1275538 TTTTTTTCTTTTT
1 TCTTTTT-TTTTC
1275551 TCTTTTCTTTTT-
1 TCTTTT-TTTTTC
1275563 TCTTTTCTTTTT-
1 TCTTTT-TTTTTC
1275575 TCTTTTTTTTTTC
1 TC-TTTTTTTTTC
1275588 TCTTTTTTCTGCTTC
1 TCTTTTTT-T--TTC
1275603 TCTTTTT
1 TCTTTTT
1275610 ATTCTTGATT
Statistics
Matches: 78, Mismatches: 6, Indels: 19
0.76 0.06 0.18
Matches are distributed among these distances:
10 4 0.05
11 6 0.08
12 35 0.45
13 22 0.28
14 1 0.01
15 10 0.13
ACGTcount: A:0.01, C:0.16, G:0.03, T:0.80
Consensus pattern (12 bp):
TCTTTTTTTTTC
Found at i:1275609 original size:35 final size:31
Alignment explanation
Indices: 1275502--1275597 Score: 110
Period size: 32 Copynumber: 3.1 Consensus size: 31
1275492 CATATGTGTC
*
1275502 TTCTTTTCTTTTTTC---TTTATTTTCTTTT
1 TTCTTTTCTTTTTTCTTTTTTCTTTTCTTTT
*
1275530 GTT-TTTGCTTTTTTTCTTTTTTCTTTTCTTTT
1 -TTCTTTTC-TTTTTTCTTTTTTCTTTTCTTTT
*
1275562 TTCTTTTCTTTTTTCTTTTTTTTTTCTCTTTT
1 TTCTTTTCTTTTTTCTTTTTTCTTT-TCTTTT
1275594 TTCT
1 TTCT
1275598 GCTTCTCTTT
Statistics
Matches: 57, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
28 4 0.07
29 9 0.16
31 18 0.32
32 26 0.46
ACGTcount: A:0.01, C:0.15, G:0.02, T:0.82
Consensus pattern (31 bp):
TTCTTTTCTTTTTTCTTTTTTCTTTTCTTTT
Found at i:1275615 original size:24 final size:21
Alignment explanation
Indices: 1275500--1275615 Score: 78
Period size: 24 Copynumber: 5.2 Consensus size: 21
1275490 TGCATATGTG
*
1275500 TCTTCTTTTCTTTTTTCTTTATTT
1 TCTT-TTTTC-TTTCTCTTT-TTT
*
1275524 TCTTTTGTT-TTT-GCTTTTTT
1 TCTTTT-TTCTTTCTCTTTTTT
*
1275544 TCTTTTTTCTTTTCTTTTTTCTTT
1 TCTTTTTTC-TTTC-TCTTT-TTT
1275568 TCTTTTTTCTTT-T-TTTTTT
1 TCTTTTTTCTTTCTCTTTTTT
1275587 CTCTTTTTTCTGCTTCTCTTTTTAT
1 -TCTTTTTTCT--TTCTCTTTTT-T
1275612 TCTT
1 TCTT
1275616 GATTGGATCT
Statistics
Matches: 77, Mismatches: 3, Indels: 24
0.74 0.03 0.23
Matches are distributed among these distances:
19 5 0.06
20 22 0.29
21 8 0.10
22 5 0.06
23 9 0.12
24 27 0.35
25 1 0.01
ACGTcount: A:0.02, C:0.16, G:0.03, T:0.79
Consensus pattern (21 bp):
TCTTTTTTCTTTCTCTTTTTT
Found at i:1276081 original size:21 final size:21
Alignment explanation
Indices: 1276055--1276094 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1276045 GACTATCGCA
1276055 TTGCGATTTCCCAAATTCGTG
1 TTGCGATTTCCCAAATTCGTG
* *
1276076 TTGCGATTTTCCTAATTCG
1 TTGCGATTTCCCAAATTCG
1276095 CAATGCGAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.17, C:0.23, G:0.17, T:0.42
Consensus pattern (21 bp):
TTGCGATTTCCCAAATTCGTG
Found at i:1276101 original size:21 final size:21
Alignment explanation
Indices: 1276028--1276102 Score: 55
Period size: 21 Copynumber: 3.6 Consensus size: 21
1276018 CAGTTTCCAG
* *
1276028 ATTCGCAACGCGATTTTGACT-
1 ATTCGCAATGCGATTTT-CCTA
* * *
1276049 A-TCGCATTGCGATTTCCCAA
1 ATTCGCAATGCGATTTTCCTA
***
1276069 ATTCGTGTTGCGATTTTCCTA
1 ATTCGCAATGCGATTTTCCTA
1276090 ATTCGCAATGCGA
1 ATTCGCAATGCGA
1276103 ATACGTAAAT
Statistics
Matches: 40, Mismatches: 12, Indels: 4
0.71 0.21 0.07
Matches are distributed among these distances:
19 1 0.03
20 13 0.32
21 26 0.65
ACGTcount: A:0.23, C:0.24, G:0.19, T:0.35
Consensus pattern (21 bp):
ATTCGCAATGCGATTTTCCTA
Found at i:1276117 original size:20 final size:20
Alignment explanation
Indices: 1276092--1276203 Score: 116
Period size: 20 Copynumber: 5.5 Consensus size: 20
1276082 TTTTCCTAAT
*
1276092 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGATTACGTAAA
* ** *
1276112 TCGCAACGCGGATTTGGAAAA
1 TCGCAATGC-GATTACGTAAA
* *
1276133 TCACAATGCGATTACATAAA
1 TCGCAATGCGATTACGTAAA
**
1276153 TCGCAACACGATTACGTAAA
1 TCGCAATGCGATTACGTAAA
* *
1276173 TCGTAAGGCGATTACGTAAA
1 TCGCAATGCGATTACGTAAA
1276193 TCGCAATGCGA
1 TCGCAATGCGA
1276204 GATTCTGACT
Statistics
Matches: 71, Mismatches: 20, Indels: 2
0.76 0.22 0.02
Matches are distributed among these distances:
20 57 0.80
21 14 0.20
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.21
Consensus pattern (20 bp):
TCGCAATGCGATTACGTAAA
Found at i:1277000 original size:21 final size:21
Alignment explanation
Indices: 1276934--1277000 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
1276924 GTGAATCGGG
1276934 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAATGGTGGGAGGGGA
* * * ** * *
1276954 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAATGGTGGGAGGGGA
1276976 CTCTTGAATGGTGGGAGGGGA
1 CTCTTGAATGGTGGGAGGGGA
1276997 CTCT
1 CTCT
1277001 CGAGGAATGA
Statistics
Matches: 31, Mismatches: 14, Indels: 2
0.66 0.30 0.04
Matches are distributed among these distances:
21 29 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.19, G:0.36, T:0.25
Consensus pattern (21 bp):
CTCTTGAATGGTGGGAGGGGA
Found at i:1278965 original size:14 final size:14
Alignment explanation
Indices: 1278946--1279002 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
1278936 GCGAAATGAA
1278946 AATCGCAACGAGAG
1 AATCGCAACGAGAG
* *
1278960 AATCGCAACGCGAAATTAA
1 AATCGCAA--CG--A-GAG
1278979 AATCGCAACGAGAG
1 AATCGCAACGAGAG
1278993 AATCGCAACG
1 AATCGCAACG
1279003 CGAAATGAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
14 19 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 9 0.26
ACGTcount: A:0.44, C:0.23, G:0.23, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:1278974 original size:33 final size:33
Alignment explanation
Indices: 1278932--1279019 Score: 167
Period size: 33 Copynumber: 2.7 Consensus size: 33
1278922 ATGACTATCA
1278932 CAACGCGAAATGAAAATCGCAACGAGAGAATCG
1 CAACGCGAAATGAAAATCGCAACGAGAGAATCG
*
1278965 CAACGCGAAATTAAAATCGCAACGAGAGAATCG
1 CAACGCGAAATGAAAATCGCAACGAGAGAATCG
1278998 CAACGCGAAATGAAAATCGCAA
1 CAACGCGAAATGAAAATCGCAA
1279020 TGCGATTTTG
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 53 1.00
ACGTcount: A:0.47, C:0.22, G:0.22, T:0.10
Consensus pattern (33 bp):
CAACGCGAAATGAAAATCGCAACGAGAGAATCG
Found at i:1278984 original size:19 final size:19
Alignment explanation
Indices: 1278880--1279024 Score: 105
Period size: 19 Copynumber: 8.1 Consensus size: 19
1278870 TCTTTTGGTT
*
1278880 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
**
1278899 GAGAATGACTAT-GCAACGC
1 GA-AATGAAAATCGCAACGC
** *
1278918 GGAAATGACTATCACAACGC
1 -GAAATGAAAATCGCAACGC
1278938 GAAATGAAAATCGCAA--C
1 GAAATGAAAATCGCAACGC
*
1278955 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
1278971 GAAATTAAAATCGCAA--C
1 GAAATGAAAATCGCAACGC
*
1278988 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
1279004 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
1279023 GA
1 GA
1279025 TTTTGGATTC
Statistics
Matches: 99, Mismatches: 14, Indels: 26
0.71 0.10 0.19
Matches are distributed among these distances:
14 19 0.19
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 53 0.54
20 15 0.15
ACGTcount: A:0.45, C:0.20, G:0.23, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:1279069 original size:33 final size:33
Alignment explanation
Indices: 1279032--1279100 Score: 120
Period size: 33 Copynumber: 2.1 Consensus size: 33
1279022 CGATTTTGGA
*
1279032 TTCGCGTTGCGATTATCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTATCTCGTTGCAATTTTCAT
*
1279065 TTCGCGTTGCGATTCTCTCGTTGCAATTTTCAT
1 TTCGCGTTGCGATTATCTCGTTGCAATTTTCAT
1279098 TTC
1 TTC
1279101 TCTCGTTGCG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.12, C:0.23, G:0.19, T:0.46
Consensus pattern (33 bp):
TTCGCGTTGCGATTATCTCGTTGCAATTTTCAT
Found at i:1279103 original size:21 final size:21
Alignment explanation
Indices: 1279077--1279155 Score: 85
Period size: 20 Copynumber: 3.9 Consensus size: 21
1279067 CGCGTTGCGA
*
1279077 TTCTCTCGTTGCAATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
**
1279098 TTCTCTCGTTGCGATAGTCAT
1 TTCTCTCGTTGCGATTTTCAT
1279119 TT-TCGT-GTTGCGATTTTCAT
1 TTCTC-TCGTTGCGATTTTCAT
1279139 TT-TCAT-GTTGCGATTTT
1 TTCTC-TCGTTGCGATTTT
1279156 AAGTTTAGAA
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
20 30 0.59
21 21 0.41
ACGTcount: A:0.13, C:0.19, G:0.16, T:0.52
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:1279717 original size:20 final size:20
Alignment explanation
Indices: 1279692--1279884 Score: 192
Period size: 20 Copynumber: 9.6 Consensus size: 20
1279682 CTTTAAAAAT
1279692 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
1279712 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
*
1279732 TGTCGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
* * * *
1279753 AGCATTGCGATTTACGTATT
1 CGCGTTGCGATTTACGGATA
* **
1279773 CTCGTTGCGATTTATAGATA
1 CGCGTTGCGATTTACGGATA
* *
1279793 CGCGTTGCGATTTACGTATT
1 CGCGTTGCGATTTACGGATA
*
1279813 CTCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
1279833 CGCGTTGCAATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
*
1279853 TGTCGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
*
1279874 CTCGTTGCGAT
1 CGCGTTGCGAT
1279885 AGTCAGAATC
Statistics
Matches: 137, Mismatches: 30, Indels: 12
0.77 0.17 0.07
Matches are distributed among these distances:
20 105 0.77
21 32 0.23
ACGTcount: A:0.19, C:0.18, G:0.25, T:0.38
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:1279778 original size:40 final size:41
Alignment explanation
Indices: 1279694--1279884 Score: 296
Period size: 40 Copynumber: 4.7 Consensus size: 41
1279684 TTAAAAATCG
*
1279694 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
* *
1279735 CGTTGCGATTTACGGATAAGCATTGCGA-TTTACGTATTCT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
**
1279775 CGTTGCGATTTATAGATACGCGTTGCGA-TTTACGTATTCT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
* *
1279815 CGTTGCGATTTACGGATACGCGTTGCAATTTTACGTATTGT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
*
1279856 CGTTGCGATTTACGGATACTCGTTGCGAT
1 CGTTGCGATTTACGGATACGCGTTGCGAT
1279885 AGTCAGAATC
Statistics
Matches: 136, Mismatches: 13, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
40 72 0.53
41 64 0.47
ACGTcount: A:0.19, C:0.18, G:0.25, T:0.38
Consensus pattern (41 bp):
CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
Found at i:1279908 original size:121 final size:121
Alignment explanation
Indices: 1279691--1279945 Score: 347
Period size: 121 Copynumber: 2.1 Consensus size: 121
1279681 GCTTTAAAAA
*
1279691 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGTCGTTGCGATTTACGGATAAGC
1 TCGCGTTGCGATTTACGGATACGCGTTGCAATTTTACGTATTGTCGTTGCGATTTACGGATAAGC
* * * *
1279756 ATTGCGATTTACGTATTCTCGTTGCGATTTATA-GATACGCGTTGCGATTTACGTAT
66 ATTGCGATTCACGTAATCTCATTGCGATTTATATG-TACGCGTTGCGATTTACATAT
* **
1279812 TCTCGTTGCGATTTACGGATACGCGTTGCAATTTTACGTATTGTCGTTGCGATTTACGGATACTC
1 TCGCGTTGCGATTTACGGATACGCGTTGCAATTTTACGTATTGTCGTTGCGATTTACGGATAAGC
* * *
1279877 GTTGCGATAGTCA-G-AATCGT-ATTGCGATTTATATGTTCGCGTTGCGATTTTCATAT
66 ATTGCGAT--TCACGTAATC-TCATTGCGATTTATATGTACGCGTTGCGATTTACATAT
1279933 TCGCGTTGCGATT
1 TCGCGTTGCGATT
1279946 ATGGAAAATC
Statistics
Matches: 118, Mismatches: 12, Indels: 8
0.86 0.09 0.06
Matches are distributed among these distances:
121 113 0.96
122 3 0.03
123 2 0.02
ACGTcount: A:0.19, C:0.18, G:0.24, T:0.39
Consensus pattern (121 bp):
TCGCGTTGCGATTTACGGATACGCGTTGCAATTTTACGTATTGTCGTTGCGATTTACGGATAAGC
ATTGCGATTCACGTAATCTCATTGCGATTTATATGTACGCGTTGCGATTTACATAT
Found at i:1279921 original size:20 final size:20
Alignment explanation
Indices: 1279898--1279945 Score: 71
Period size: 20 Copynumber: 2.4 Consensus size: 20
1279888 CAGAATCGTA
*
1279898 TTGCGATTTAT-ATGTTCGCG
1 TTGCGATTT-TCATATTCGCG
1279918 TTGCGATTTTCATATTCGCG
1 TTGCGATTTTCATATTCGCG
1279938 TTGCGATT
1 TTGCGATT
1279946 ATGGAAAATC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 1 0.04
20 25 0.96
ACGTcount: A:0.15, C:0.17, G:0.23, T:0.46
Consensus pattern (20 bp):
TTGCGATTTTCATATTCGCG
Found at i:1279942 original size:40 final size:40
Alignment explanation
Indices: 1279691--1279945 Score: 232
Period size: 40 Copynumber: 6.3 Consensus size: 40
1279681 GCTTTAAAAA
*
1279691 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTTACGTAT
1 TCGCGTTGCGATTTAAGGATACGCGTTGCGATTTT-CGTAT
* * * *
1279732 T-GTCGTTGCGATTTACGGATAAGCATTGCGATTTACGTAT
1 TCG-CGTTGCGATTTAAGGATACGCGTTGCGATTTTCGTAT
* *
1279772 TCTCGTTGCGATTTATA-GATACGCGTTGCGATTTACGTAT
1 TCGCGTTGCGATTTA-AGGATACGCGTTGCGATTTTCGTAT
* * *
1279812 TCTCGTTGCGATTTACGGATACGCGTTGCAATTTTACGTAT
1 TCGCGTTGCGATTTAAGGATACGCGTTGCGATTTT-CGTAT
* * ** *
1279853 T-GTCGTTGCGATTTACGGATACTCGTTGCGATAGTCAG-AA
1 TCG-CGTTGCGATTTAAGGATACGCGTTGCGATTTTC-GTAT
** * * *
1279893 TCGTATTGCGATTTATATG-TTCGCGTTGCGATTTTCATAT
1 TCGCGTTGCGATTTA-AGGATACGCGTTGCGATTTTCGTAT
1279933 TCGCGTTGCGATT
1 TCGCGTTGCGATT
1279946 ATGGAAAATC
Statistics
Matches: 176, Mismatches: 28, Indels: 21
0.78 0.12 0.09
Matches are distributed among these distances:
40 109 0.62
41 67 0.38
ACGTcount: A:0.19, C:0.18, G:0.24, T:0.39
Consensus pattern (40 bp):
TCGCGTTGCGATTTAAGGATACGCGTTGCGATTTTCGTAT
Found at i:1280044 original size:20 final size:20
Alignment explanation
Indices: 1279974--1280048 Score: 64
Period size: 20 Copynumber: 3.7 Consensus size: 20
1279964 AATTTGTACT
* **
1279974 ATCGCATTGCGATTCTTCATA
1 ATCGCGTTGCGATTC-TGGTA
1279995 ATCGCGTTGCGATTCTGGTA
1 ATCGCGTTGCGATTCTGGTA
**
1280015 A-CTGATTTGCGATTCTGG-A
1 ATC-GCGTTGCGATTCTGGTA
1280034 GATCGCGTTGCGATT
1 -ATCGCGTTGCGATT
1280049 TTTATTTCGC
Statistics
Matches: 44, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
19 2 0.05
20 27 0.61
21 15 0.34
ACGTcount: A:0.19, C:0.20, G:0.25, T:0.36
Consensus pattern (20 bp):
ATCGCGTTGCGATTCTGGTA
Found at i:1281907 original size:16 final size:16
Alignment explanation
Indices: 1281846--1281905 Score: 93
Period size: 16 Copynumber: 3.8 Consensus size: 16
1281836 ATGAAAAATC
1281846 CTACCCCACATGATAT
1 CTACCCCACATGATAT
1281862 CTACCCCACATGATAT
1 CTACCCCACATGATAT
*
1281878 CTACCCCACATGCTAT
1 CTACCCCACATGATAT
* *
1281894 ATACCCGACATG
1 CTACCCCACATG
1281906 CTTATTATTT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 41 1.00
ACGTcount: A:0.30, C:0.38, G:0.08, T:0.23
Consensus pattern (16 bp):
CTACCCCACATGATAT
Found at i:1282951 original size:20 final size:21
Alignment explanation
Indices: 1282900--1282951 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
1282890 AGTAAAAGGG
1282900 AAAAGAGAAAATAATAAAAAA
1 AAAAGAGAAAATAATAAAAAA
* *
1282921 AAAAGATAAAATCAA-AAAAAC
1 AAAAGAGAAAAT-AATAAAAAA
1282942 AAAAG-GAAAA
1 AAAAGAGAAAA
1282952 AAAAGAGAAC
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 4 0.15
21 21 0.78
22 2 0.07
ACGTcount: A:0.79, C:0.04, G:0.10, T:0.08
Consensus pattern (21 bp):
AAAAGAGAAAATAATAAAAAA
Found at i:1283117 original size:19 final size:19
Alignment explanation
Indices: 1283073--1283124 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
1283063 TGAAATTGAG
*
1283073 TAAAAAATAATAAAAAAGA
1 TAAAAAATAATAAAAAACA
*
1283092 -AATAAAAGAATAAAAAACA
1 TAA-AAAATAATAAAAAACA
1283111 TAAAAAATAATAAA
1 TAAAAAATAATAAA
1283125 TAAAAAAACG
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
18 2 0.07
19 24 0.86
20 2 0.07
ACGTcount: A:0.79, C:0.02, G:0.04, T:0.15
Consensus pattern (19 bp):
TAAAAAATAATAAAAAACA
Found at i:1283145 original size:38 final size:38
Alignment explanation
Indices: 1283074--1283151 Score: 88
Period size: 38 Copynumber: 2.1 Consensus size: 38
1283064 GAAATTGAGT
* *
1283074 AAAAAATAATAAAAAAGAAATAAAAGAATAAAAAACAT
1 AAAAAATAATAAAAAAGAAATAAAAGAAGAAAAAAAAT
* *
1283112 AAAAAATAATAAATAAA-AAA-ACGAAGTAGAAAAAAAAT
1 AAAAAATAATAAA-AAAGAAATA-AAAGAAGAAAAAAAAT
1283150 AA
1 AA
1283152 TAAGGGTTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
37 1 0.03
38 30 0.88
39 3 0.09
ACGTcount: A:0.78, C:0.03, G:0.06, T:0.13
Consensus pattern (38 bp):
AAAAAATAATAAAAAAGAAATAAAAGAAGAAAAAAAAT
Found at i:1285717 original size:5 final size:5
Alignment explanation
Indices: 1285707--1285761 Score: 58
Period size: 5 Copynumber: 10.6 Consensus size: 5
1285697 CTTCAAACGT
*
1285707 TATTA TATTA TATGA TA-TA TATTTA TATTA TAAATTA TATTA TATTA
1 TATTA TATTA TATTA TATTA TA-TTA TATTA T--ATTA TATTA TATTA
*
1285754 TATAA TAT
1 TATTA TAT
1285762 ATTTATTTAC
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
4 3 0.07
5 31 0.72
6 4 0.09
7 5 0.12
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.55
Consensus pattern (5 bp):
TATTA
Found at i:1285757 original size:12 final size:12
Alignment explanation
Indices: 1285707--1285764 Score: 57
Period size: 12 Copynumber: 4.8 Consensus size: 12
1285697 CTTCAAACGT
1285707 TATTATATTATA
1 TATTATATTATA
1285719 TGATATATATT-TA
1 T-AT-TATATTATA
*
1285732 TATTATA-AATTA
1 TATTATATTA-TA
1285744 TATTATATTATA
1 TATTATATTATA
*
1285756 TAATATATT
1 TATTATATT
1285765 TATTTACATT
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
11 4 0.11
12 22 0.58
13 6 0.16
14 6 0.16
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (12 bp):
TATTATATTATA
Found at i:1286108 original size:15 final size:14
Alignment explanation
Indices: 1286088--1286148 Score: 52
Period size: 15 Copynumber: 4.0 Consensus size: 14
1286078 ATATTTTATA
1286088 TTTTATCTTATTTTC
1 TTTTAT-TTATTTTC
1286103 TTTTATTT-TTTACTC
1 TTTTATTTATTT--TC
*
1286118 TTTTATATTATTATTA
1 TTTTAT-TTATT-TTC
1286134 TATTTATTTATTTTC
1 T-TTTATTTATTTTC
1286149 ATTATTTTGT
Statistics
Matches: 38, Mismatches: 2, Indels: 12
0.73 0.04 0.23
Matches are distributed among these distances:
13 3 0.08
14 2 0.05
15 16 0.42
16 9 0.24
17 7 0.18
18 1 0.03
ACGTcount: A:0.20, C:0.08, G:0.00, T:0.72
Consensus pattern (14 bp):
TTTTATTTATTTTC
Found at i:1286174 original size:22 final size:22
Alignment explanation
Indices: 1286074--1286179 Score: 50
Period size: 22 Copynumber: 4.9 Consensus size: 22
1286064 TATGTATATA
1286074 TATTATATT-TTA-TATTTTATCT
1 TATT-TATTATTATTATTTTAT-T
*
1286096 TATTT-TCTTTTATT-TTTTACTCT
1 TATTTAT-TATTATTATTTTA-T-T
1286119 T-TTATATTATTATTAT---ATT
1 TATT-TATTATTATTATTTTATT
*
1286138 TATTTATT-TTCATTATTTTGTT
1 TATTTATTATT-ATTATTTTATT
*
1286160 TCTTTATTATTATTAATTTT
1 TATTTATTATTATT-ATTTT
1286180 CTCTCTCTCA
Statistics
Matches: 67, Mismatches: 3, Indels: 27
0.69 0.03 0.28
Matches are distributed among these distances:
18 2 0.03
19 11 0.16
20 4 0.06
21 3 0.04
22 26 0.39
23 19 0.28
24 2 0.03
ACGTcount: A:0.23, C:0.06, G:0.01, T:0.71
Consensus pattern (22 bp):
TATTTATTATTATTATTTTATT
Found at i:1286413 original size:16 final size:16
Alignment explanation
Indices: 1286392--1286425 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
1286382 GTCATATATA
1286392 TTTATTTTATTTTGTT
1 TTTATTTTATTTTGTT
*
1286408 TTTATTTTGTTTTGTT
1 TTTATTTTATTTTGTT
1286424 TT
1 TT
1286426 CTTTGTTTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.09, C:0.00, G:0.09, T:0.82
Consensus pattern (16 bp):
TTTATTTTATTTTGTT
Found at i:1286432 original size:14 final size:14
Alignment explanation
Indices: 1286413--1286462 Score: 66
Period size: 14 Copynumber: 3.6 Consensus size: 14
1286403 TTGTTTTTAT
1286413 TTTGTTTTGTTTTC
1 TTTGTTTTGTTTTC
1286427 TTTGTTTTGTTTTC
1 TTTGTTTTGTTTTC
* *
1286441 TCT-TTTTGTTTTA
1 TTTGTTTTGTTTTC
1286454 TTGTGTTTT
1 TT-TGTTTT
1286463 TATTTTCTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
13 10 0.32
14 17 0.55
15 4 0.13
ACGTcount: A:0.02, C:0.06, G:0.14, T:0.78
Consensus pattern (14 bp):
TTTGTTTTGTTTTC
Found at i:1287597 original size:4 final size:4
Alignment explanation
Indices: 1287588--1287613 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
1287578 CCTTTCGTCG
1287588 TTAT TTAT TTAT TTAT TTAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TT
1287614 TAATTTTACT
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:1296922 original size:17 final size:17
Alignment explanation
Indices: 1296887--1296931 Score: 56
Period size: 17 Copynumber: 2.7 Consensus size: 17
1296877 TCCTAAGTCG
* *
1296887 AAGAAAGAAAA-AGAAA
1 AAGAAAAAAAACAAAAA
1296903 AAGAAAAAAAACAAAAA
1 AAGAAAAAAAACAAAAA
*
1296920 AAGAATAAAAAC
1 AAGAAAAAAAAC
1296932 GTTTAGGGTG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
16 10 0.40
17 15 0.60
ACGTcount: A:0.82, C:0.04, G:0.11, T:0.02
Consensus pattern (17 bp):
AAGAAAAAAAACAAAAA
Found at i:1298344 original size:110 final size:106
Alignment explanation
Indices: 1298119--1298386 Score: 304
Period size: 110 Copynumber: 2.5 Consensus size: 106
1298109 GACGAAGGGG
* * * *** * *
1298119 TTTCCCAGTTTCAGAGCCAATTTTAACTTCACAACAAAGGATATTGGACCCAAGACAACACAAAC
1 TTTCCCAGTTCCAGAGCCAATTTCAACATCACAGTGAAGGATATTGGACTCGAGACAACACAAAC
1298184 TCAACTTCACAACGAAGGGGCAACTGATTGTCAACAAACAA
66 TCAACTTCACAACGAAGGGGCAACTGATTGTCAACAAACAA
** * * * *
1298225 TTTTTCAGTTTCATTCAGAGTCAATTTCAACATCATAGTGAAGGATGTTGGACTCGAGACAGCAC
1 TTTCCCAG-TTC---CAGAGCCAATTTCAACATCACAGTGAAGGATATTGGACTCGAGACAACAC
* **
1298290 AAGCTCAACTTCACAACGAAGGGGCGGCTGACTT-TCAACAAACAA
62 AAACTCAACTTCACAACGAAGGGGCAACTGA-TTGTCAACAAACAA
* * *
1298335 TTTCCCAGTTCCAGAGCCAATTTCAACTTCACGGTGGAGGATATTGGACTCG
1 TTTCCCAGTTCCAGAGCCAATTTCAACATCACAGTGAAGGATATTGGACTCG
1298387 GAACAATACA
Statistics
Matches: 132, Mismatches: 25, Indels: 10
0.79 0.15 0.06
Matches are distributed among these distances:
106 41 0.31
107 2 0.02
109 3 0.02
110 84 0.64
111 2 0.02
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.24
Consensus pattern (106 bp):
TTTCCCAGTTCCAGAGCCAATTTCAACATCACAGTGAAGGATATTGGACTCGAGACAACACAAAC
TCAACTTCACAACGAAGGGGCAACTGATTGTCAACAAACAA
Found at i:1299144 original size:12 final size:13
Alignment explanation
Indices: 1299122--1299159 Score: 53
Period size: 12 Copynumber: 3.1 Consensus size: 13
1299112 TATTATATGA
*
1299122 TATATATTTATAT
1 TATATAATTATAT
1299135 TATA-AATTATAT
1 TATATAATTATAT
1299147 TATATAA-TATAT
1 TATATAATTATAT
1299159 T
1 T
1299160 CATCTATATA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
12 17 0.74
13 6 0.26
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
TATATAATTATAT
Found at i:1299145 original size:20 final size:20
Alignment explanation
Indices: 1299109--1299157 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 20
1299099 TCAAACGTTA
*
1299109 TTATATTATATGATATATAT
1 TTATATTATATAATATATAT
1299129 TTATATTATA-AAT-TATA-
1 TTATATTATATAATATATAT
*
1299146 TTATATAATATA
1 TTATATTATATA
1299158 TTCATCTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
17 9 0.35
18 5 0.19
19 2 0.08
20 10 0.38
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (20 bp):
TTATATTATATAATATATAT
Found at i:1299562 original size:18 final size:19
Alignment explanation
Indices: 1299539--1299586 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 19
1299529 CTTTTATATT
1299539 ATTATTATATTTATTT-TC
1 ATTATTATATTTATTTATC
* * *
1299557 ATTATTTTATTTCTTTATT
1 ATTATTATATTTATTTATC
1299576 ATTATTA-ATTT
1 ATTATTATATTT
1299587 TCTCTCTCTC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
18 18 0.72
19 7 0.28
ACGTcount: A:0.27, C:0.04, G:0.00, T:0.69
Consensus pattern (19 bp):
ATTATTATATTTATTTATC
Found at i:1305656 original size:19 final size:19
Alignment explanation
Indices: 1305629--1305695 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
1305619 ATGACCAACA
* *
1305629 AAATTGCAATGCGATCTCT
1 AAATCGCAACGCGATCTCT
*
1305648 AAATCGCAACGCGATCTAT
1 AAATCGCAACGCGATCTCT
*
1305667 AAATCGCAACGCGATCTCC
1 AAATCGCAACGCGATCTCT
1305686 AATATCGCAA
1 AA-ATCGCAA
1305696 ATCAGTTTCC
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
19 35 0.83
20 7 0.17
ACGTcount: A:0.36, C:0.27, G:0.15, T:0.22
Consensus pattern (19 bp):
AAATCGCAACGCGATCTCT
Found at i:1305734 original size:20 final size:20
Alignment explanation
Indices: 1305711--1305820 Score: 71
Period size: 20 Copynumber: 5.4 Consensus size: 20
1305701 TTTCCAGATT
*
1305711 CGCAACGCGATTTTGACTAA
1 CGCAACGCGATTATGACTAA
* *
1305731 CGCAACACGATAAT-ACATAA
1 CGCAACGCGATTATGAC-TAA
* * *
1305751 TCGCAACGAGATTCTGACTAT
1 -CGCAACGCGATTATGACTAA
*
1305772 CGCAACGCGATAAT-ACATAA
1 CGCAACGCGATTATGAC-TAA
* * **
1305792 TCGTAACGCGATTCTGACTGT
1 -CGCAACGCGATTATGACTAA
1305813 CGCAACGC
1 CGCAACGC
1305821 TGAATTTCAA
Statistics
Matches: 66, Mismatches: 18, Indels: 12
0.69 0.19 0.12
Matches are distributed among these distances:
19 4 0.06
20 34 0.52
21 24 0.36
22 4 0.06
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.22
Consensus pattern (20 bp):
CGCAACGCGATTATGACTAA
Found at i:1305756 original size:21 final size:21
Alignment explanation
Indices: 1305731--1305803 Score: 62
Period size: 21 Copynumber: 3.5 Consensus size: 21
1305721 TTTTGACTAA
1305731 CGCAACACGATAATACATAAT
1 CGCAACACGATAATACATAAT
**
1305752 CGCAACGA-GATTCTGAC-T-AT
1 CGCAAC-ACGATAAT-ACATAAT
*
1305772 CGCAACGCGATAATACATAAT
1 CGCAACACGATAATACATAAT
* *
1305793 CGTAACGCGAT
1 CGCAACACGAT
1305804 TCTGACTGTC
Statistics
Matches: 41, Mismatches: 6, Indels: 10
0.72 0.11 0.18
Matches are distributed among these distances:
19 2 0.05
20 13 0.32
21 23 0.56
22 3 0.07
ACGTcount: A:0.38, C:0.25, G:0.16, T:0.21
Consensus pattern (21 bp):
CGCAACACGATAATACATAAT
Found at i:1305816 original size:41 final size:41
Alignment explanation
Indices: 1305710--1305820 Score: 168
Period size: 41 Copynumber: 2.7 Consensus size: 41
1305700 GTTTCCAGAT
* * *
1305710 TCGCAACGCGATTTTGACTAACGCAACACGATAATACATAA
1 TCGCAACGCGATTCTGACTATCGCAACGCGATAATACATAA
*
1305751 TCGCAACGAGATTCTGACTATCGCAACGCGATAATACATAA
1 TCGCAACGCGATTCTGACTATCGCAACGCGATAATACATAA
* *
1305792 TCGTAACGCGATTCTGACTGTCGCAACGC
1 TCGCAACGCGATTCTGACTATCGCAACGC
1305821 TGAATTTCAA
Statistics
Matches: 63, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 63 1.00
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.23
Consensus pattern (41 bp):
TCGCAACGCGATTCTGACTATCGCAACGCGATAATACATAA
Found at i:1306894 original size:12 final size:13
Alignment explanation
Indices: 1306879--1306911 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
1306869 AGAAGAAAAA
1306879 GAAGAAA-TCCCC
1 GAAGAAAGTCCCC
1306891 GAAGAAAAGTCCCC
1 GAAG-AAAGTCCCC
1306905 GAAGAAA
1 GAAGAAA
1306912 ATGCCACGGG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 4 0.21
13 6 0.32
14 9 0.47
ACGTcount: A:0.48, C:0.24, G:0.21, T:0.06
Consensus pattern (13 bp):
GAAGAAAGTCCCC
Found at i:1306905 original size:14 final size:14
Alignment explanation
Indices: 1306886--1306912 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1306876 AAAGAAGAAA
1306886 TCCCCGAAGAAAAG
1 TCCCCGAAGAAAAG
1306900 TCCCCGAAGAAAA
1 TCCCCGAAGAAAA
1306913 TGCCACGGGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.30, G:0.19, T:0.07
Consensus pattern (14 bp):
TCCCCGAAGAAAAG
Found at i:1308153 original size:13 final size:13
Alignment explanation
Indices: 1308135--1308160 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1308125 GTTTGAAAGA
1308135 TGGTCAAGAGTAC
1 TGGTCAAGAGTAC
1308148 TGGTCAAGAGTAC
1 TGGTCAAGAGTAC
1308161 ATCAACTTGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.31, T:0.23
Consensus pattern (13 bp):
TGGTCAAGAGTAC
Found at i:1308985 original size:18 final size:18
Alignment explanation
Indices: 1308962--1308996 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1308952 AGAAAAAGGC
*
1308962 AATCAAAATCGCAATCAA
1 AATCAAAATCCCAATCAA
1308980 AATCAAAATCCCAATCA
1 AATCAAAATCCCAATCA
1308997 CAACCGGCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.54, C:0.26, G:0.03, T:0.17
Consensus pattern (18 bp):
AATCAAAATCCCAATCAA
Found at i:1309307 original size:140 final size:140
Alignment explanation
Indices: 1309055--1309617 Score: 1072
Period size: 140 Copynumber: 4.0 Consensus size: 140
1309045 GCAAACATTG
*
1309055 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
1 TATTACGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
*
1309120 TTAAACATTGCTATGATCTGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACG
66 TTGAACATTGCTATGATCTGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACG
1309185 CGAATTTGAC
131 CGAATTTGAC
1309195 TATTACGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
1 TATTACGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
1309260 TTGAACATTGCTATGATCTGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACG
66 TTGAACATTGCTATGATCTGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACG
*
1309325 TGAATTTGAC
131 CGAATTTGAC
1309335 TATTACGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
1 TATTACGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
*
1309400 TTGAACATTACTATGATCTGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACG
66 TTGAACATTGCTATGATCTGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACG
1309465 CGAATTTGAC
131 CGAATTTGAC
*
1309475 TATTACGTGTATTTTATGTGTAAACTTTTATCATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
1 TATTACGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
*
1309540 TTGAGCATTGCTATGATCTGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACG
66 TTGAACATTGCTATGATCTGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACG
1309605 CGAATTTGAC
131 CGAATTTGAC
1309615 TAT
1 TAT
1309618 CAAAACGCGA
Statistics
Matches: 415, Mismatches: 8, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
140 415 1.00
ACGTcount: A:0.28, C:0.14, G:0.15, T:0.43
Consensus pattern (140 bp):
TATTACGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
TTGAACATTGCTATGATCTGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACG
CGAATTTGAC
Found at i:1309744 original size:60 final size:60
Alignment explanation
Indices: 1309595--1309817 Score: 245
Period size: 54 Copynumber: 3.9 Consensus size: 60
1309585 TTCATTTGAA
** *
1309595 TATCGCAACGCGAATTTGACTATCAAAACGCGAATTTGACTATCGCAACTC-AA-A--A-
1 TATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGCAACGCGAATATGAC
*
1309650 -ATCGCAACGCGAATTTGATTATCGCAACGCGAATTTGACTATCGCAACGCGAATATGAC
1 TATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGCAACGCGAATATGAC
* * * * *
1309709 TATCGCAACACGAATTTGACTATCGCAACGGGAATTTGATTATCGCAACGGGAATTTGAC
1 TATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGCAACGCGAATATGAC
* * * *
1309769 TATCGCAACGAGAA----A--ATCGCAAAGCGTATTAGACTATCGCAACGCGAAT
1 TATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGCAACGCGAAT
1309818 TAACTTTCGC
Statistics
Matches: 144, Mismatches: 18, Indels: 13
0.82 0.10 0.07
Matches are distributed among these distances:
54 74 0.51
55 2 0.01
56 2 0.01
58 1 0.01
60 65 0.45
ACGTcount: A:0.35, C:0.22, G:0.19, T:0.23
Consensus pattern (60 bp):
TATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGCAACGCGAATATGAC
Found at i:1309819 original size:20 final size:20
Alignment explanation
Indices: 1309588--1309818 Score: 243
Period size: 20 Copynumber: 12.2 Consensus size: 20
1309578 TTACACATTC
*
1309588 ATTTGAATATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
**
1309608 ATTTGACTATCAAAACGCGA
1 ATTTGACTATCGCAACGCGA
*
1309628 ATTTGACTATCGCAACTC-A
1 ATTTGACTATCGCAACGCGA
*
1309647 A----A-AATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
1309662 ATTTGATTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
1309682 ATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* *
1309702 ATATGACTATCGCAACACGA
1 ATTTGACTATCGCAACGCGA
*
1309722 ATTTGACTATCGCAACGGGA
1 ATTTGACTATCGCAACGCGA
* *
1309742 ATTTGATTATCGCAACGGGA
1 ATTTGACTATCGCAACGCGA
*
1309762 ATTTGACTATCGCAACGAGA
1 ATTTGACTATCGCAACGCGA
* *
1309782 A----A--ATCGCAAAGCGT
1 ATTTGACTATCGCAACGCGA
*
1309796 ATTAGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
1309816 ATT
1 ATT
1309819 AACTTTCGCG
Statistics
Matches: 176, Mismatches: 23, Indels: 24
0.79 0.10 0.11
Matches are distributed among these distances:
14 19 0.11
15 3 0.02
16 1 0.01
18 1 0.01
19 3 0.02
20 149 0.85
ACGTcount: A:0.35, C:0.22, G:0.19, T:0.24
Consensus pattern (20 bp):
ATTTGACTATCGCAACGCGA
Found at i:1309960 original size:20 final size:20
Alignment explanation
Indices: 1309821--1309959 Score: 215
Period size: 20 Copynumber: 7.0 Consensus size: 20
1309811 CGCGAATTAA
* *
1309821 CTTTCGCGTTGTGATTTTGG
1 CTTTCGCATTGCGATTTTGG
1309841 CTTTCGCATTGCGATTTTGG
1 CTTTCGCATTGCGATTTTGG
1309861 CTTTCGCATTGCGATTTTGG
1 CTTTCGCATTGCGATTTTGG
*
1309881 CTTTTGCATTGCGATTTTGG
1 CTTTCGCATTGCGATTTTGG
*
1309901 CTTTCGCATTGCGATTTTTG
1 CTTTCGCATTGCGATTTTGG
* *
1309921 CTTTCGTATTGCGATTTTGA
1 CTTTCGCATTGCGATTTTGG
*
1309941 CTTTCGCATTACGATTTTG
1 CTTTCGCATTGCGATTTTG
1309960 AGTTTAGCGT
Statistics
Matches: 109, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 109 1.00
ACGTcount: A:0.11, C:0.18, G:0.23, T:0.48
Consensus pattern (20 bp):
CTTTCGCATTGCGATTTTGG
Found at i:1309973 original size:60 final size:60
Alignment explanation
Indices: 1309833--1309974 Score: 196
Period size: 60 Copynumber: 2.4 Consensus size: 60
1309823 TTCGCGTTGT
* * * *
1309833 GATTTTGGCTTTCGCATTGCGATTTTGGCTTTCGCATTGCGATTTTGGCTTTTGCATTGC
1 GATTTTGGCTTTAGCATTGCGATTTTGGCTTTCGCATTGCGATTTTGACTTTCGCATTAC
* * *
1309893 GATTTTGGCTTTCGCATTGCGATTTTTGCTTTCGTATTGCGATTTTGACTTTCGCATTAC
1 GATTTTGGCTTTAGCATTGCGATTTTGGCTTTCGCATTGCGATTTTGACTTTCGCATTAC
*
1309953 GATTTTGAG-TTTAGCGTTGCGA
1 GATTTTG-GCTTTAGCATTGCGA
1309975 AAGTGTACCT
Statistics
Matches: 74, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
60 73 0.99
61 1 0.01
ACGTcount: A:0.13, C:0.17, G:0.24, T:0.46
Consensus pattern (60 bp):
GATTTTGGCTTTAGCATTGCGATTTTGGCTTTCGCATTGCGATTTTGACTTTCGCATTAC
Found at i:1310090 original size:36 final size:36
Alignment explanation
Indices: 1310049--1310157 Score: 119
Period size: 36 Copynumber: 3.3 Consensus size: 36
1310039 TTACATTTCA
1310049 ATCAATTAAATAAGCACAAATAAGAATTATTTACAC
1 ATCAATTAAATAAGCACAAATAAGAATTATTTACAC
* * *
1310085 ATCAA-T---TAA--ACAAAT--CAACT-TTTACAA
1 ATCAATTAAATAAGCACAAATAAGAATTATTTACAC
*
1310112 ATCAATTAAACAAGCACAAATAAGAATTATTTACAC
1 ATCAATTAAATAAGCACAAATAAGAATTATTTACAC
1310148 ATCAATTAAA
1 ATCAATTAAA
1310158 CAAATCAACT
Statistics
Matches: 57, Mismatches: 7, Indels: 18
0.70 0.09 0.22
Matches are distributed among these distances:
27 11 0.19
28 4 0.07
30 6 0.11
31 2 0.04
32 3 0.05
33 6 0.11
35 4 0.07
36 21 0.37
ACGTcount: A:0.53, C:0.16, G:0.04, T:0.28
Consensus pattern (36 bp):
ATCAATTAAATAAGCACAAATAAGAATTATTTACAC
Found at i:1310134 original size:63 final size:63
Alignment explanation
Indices: 1310026--1310179 Score: 254
Period size: 63 Copynumber: 2.4 Consensus size: 63
1310016 GATTGAAATC
*
1310026 AACAAATCAACTTTTACATTTCAATCAATTAAATAAGCACAAATAAGAATTATTTACACATCAAT
1 AACAAATCAACTTTTACA----AATCAATTAAACAAGCACAAATAAGAATTATTTACACATCAAT
1310091 TA
62 TA
1310093 AACAAATCAACTTTTACAAATCAATTAAACAAGCACAAATAAGAATTATTTACACATCAATTA
1 AACAAATCAACTTTTACAAATCAATTAAACAAGCACAAATAAGAATTATTTACACATCAATTA
*
1310156 AACAAATCAACTTTTACAAGTCAA
1 AACAAATCAACTTTTACAAATCAA
1310180 CTTTTACAAA
Statistics
Matches: 85, Mismatches: 2, Indels: 4
0.93 0.02 0.04
Matches are distributed among these distances:
63 67 0.79
67 18 0.21
ACGTcount: A:0.51, C:0.18, G:0.03, T:0.29
Consensus pattern (63 bp):
AACAAATCAACTTTTACAAATCAATTAAACAAGCACAAATAAGAATTATTTACACATCAATTA
Found at i:1310179 original size:14 final size:14
Alignment explanation
Indices: 1310157--1310193 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
1310147 CATCAATTAA
1310157 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
1310171 ACAAGTCAACTTTT
1 ACAAATCAACTTTT
1310185 ACAAATCAA
1 ACAAATCAA
1310194 TTAAACAAGC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.03, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:1311657 original size:42 final size:42
Alignment explanation
Indices: 1311581--1311672 Score: 114
Period size: 42 Copynumber: 2.2 Consensus size: 42
1311571 GTGATTCGAG
*
1311581 CTCTTGAATGGTGGGAGGGACCTCTTCAACGATGACAGGGGC
1 CTCTTGAATAGTGGGAGGGACCTCTTCAACGATGACAGGGGC
* ** *
1311623 CTCTTGAATAGTGGGAAGGGACC-CTTGAGGGATGATAGGGGC
1 CTCTTGAATAGTGGG-AGGGACCTCTTCAACGATGACAGGGGC
*
1311665 CTATTGAA
1 CTCTTGAA
1311673 CGATAGGAGA
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
42 36 0.84
43 7 0.16
ACGTcount: A:0.24, C:0.17, G:0.36, T:0.23
Consensus pattern (42 bp):
CTCTTGAATAGTGGGAGGGACCTCTTCAACGATGACAGGGGC
Found at i:1312204 original size:20 final size:20
Alignment explanation
Indices: 1312179--1312222 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
1312169 AATAGTTTAT
*
1312179 GAAACTTAAAATTGCAACAC
1 GAAACTTAAAATCGCAACAC
*
1312199 GAAACTTAAAATCGCAACGC
1 GAAACTTAAAATCGCAACAC
1312219 GAAA
1 GAAA
1312223 ATGACTATCG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.50, C:0.20, G:0.14, T:0.16
Consensus pattern (20 bp):
GAAACTTAAAATCGCAACAC
Found at i:1312232 original size:20 final size:20
Alignment explanation
Indices: 1312209--1312277 Score: 93
Period size: 20 Copynumber: 3.5 Consensus size: 20
1312199 GAAACTTAAA
1312209 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* * *
1312229 ATCGCAACTCGGAAATGAAT
1 ATCGCAACGCGAAAATGACT
**
1312249 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
1312269 ATCGCAACG
1 ATCGCAACG
1312278 GGATAATCGT
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.36, C:0.25, G:0.20, T:0.19
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:1312306 original size:33 final size:33
Alignment explanation
Indices: 1312269--1312348 Score: 88
Period size: 33 Copynumber: 2.4 Consensus size: 33
1312259 GAATTTGACT
* * * * *
1312269 ATCGCAACGGGATAATCGTAATGCGAAATAAAA
1 ATCGCAACGAGAAAATCGCAACGCGAAACAAAA
*
1312302 ATCGCAACGAGAAAATCGCAACGCGAAACCAAA
1 ATCGCAACGAGAAAATCGCAACGCGAAACAAAA
* *
1312335 ATTGCAACGCGAAA
1 ATCGCAACGAGAAA
1312349 CTAAATTCGC
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.46, C:0.21, G:0.20, T:0.12
Consensus pattern (33 bp):
ATCGCAACGAGAAAATCGCAACGCGAAACAAAA
Found at i:1312318 original size:14 final size:14
Alignment explanation
Indices: 1312299--1312329 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
1312289 ATGCGAAATA
1312299 AAAATCGCAACGAG
1 AAAATCGCAACGAG
*
1312313 AAAATCGCAACGCG
1 AAAATCGCAACGAG
1312327 AAA
1 AAA
1312330 CCAAAATTGC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.52, C:0.23, G:0.19, T:0.06
Consensus pattern (14 bp):
AAAATCGCAACGAG
Found at i:1312341 original size:19 final size:19
Alignment explanation
Indices: 1312313--1312349 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
1312303 TCGCAACGAG
1312313 AAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAACC
*
1312332 AAAATTGCAACGCGAAAC
1 AAAATCGCAACGCGAAAC
1312350 TAAATTCGCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.49, C:0.27, G:0.16, T:0.08
Consensus pattern (19 bp):
AAAATCGCAACGCGAAACC
Found at i:1312431 original size:33 final size:34
Alignment explanation
Indices: 1312360--1312433 Score: 87
Period size: 33 Copynumber: 2.2 Consensus size: 34
1312350 TAAATTCGCG
* * *
1312360 TTGCGATTTTCATTTTTGCATTACGATTTTCACG
1 TTGCGATTTTCATTTTCGCATTACGATTATCACA
* * *
1312394 TTGCGATTTTTA-TTTCGCATTGCGATTATCCCA
1 TTGCGATTTTCATTTTCGCATTACGATTATCACA
1312427 TTGCGAT
1 TTGCGAT
1312434 AGTCAAATTC
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
33 23 0.68
34 11 0.32
ACGTcount: A:0.18, C:0.19, G:0.16, T:0.47
Consensus pattern (34 bp):
TTGCGATTTTCATTTTCGCATTACGATTATCACA
Found at i:1314435 original size:19 final size:20
Alignment explanation
Indices: 1314367--1314437 Score: 83
Period size: 19 Copynumber: 3.6 Consensus size: 20
1314357 AATAGTTTCT
* *
1314367 GAAACTTAAAATCGCAACAC
1 GAAACTGAAAATCGCAACGC
* **
1314387 GAAAATGACTATCGCAACGC
1 GAAACTGAAAATCGCAACGC
1314407 GAAA-TGAAAATCGCAACGC
1 GAAACTGAAAATCGCAACGC
1314426 GAAACT-AAAATC
1 GAAACTGAAAATC
1314438 ACGTTGCAAT
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
19 23 0.53
20 20 0.47
ACGTcount: A:0.48, C:0.23, G:0.15, T:0.14
Consensus pattern (20 bp):
GAAACTGAAAATCGCAACGC
Found at i:1315037 original size:20 final size:20
Alignment explanation
Indices: 1315012--1315117 Score: 124
Period size: 20 Copynumber: 5.2 Consensus size: 20
1315002 TTAGCGCAAC
*
1315012 GCGATAGTCAGAATCGCGTT
1 GCGATAGTAAGAATCGCGTT
1315032 GCGATAGTAAGAATCGCGTT
1 GCGATAGTAAGAATCGCGTT
* **
1315052 ACGATTATGT-ATTATCGCGTT
1 GCGA-TA-GTAAGAATCGCGTT
*
1315073 GCGATAGTAAGAATCGCATT
1 GCGATAGTAAGAATCGCGTT
* *
1315093 GCGATAGTCAGAATCTCGTT
1 GCGATAGTAAGAATCGCGTT
1315113 GCGAT
1 GCGAT
1315118 TTACATATTC
Statistics
Matches: 72, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
19 2 0.03
20 54 0.75
21 14 0.19
22 2 0.03
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.29
Consensus pattern (20 bp):
GCGATAGTAAGAATCGCGTT
Found at i:1315160 original size:22 final size:21
Alignment explanation
Indices: 1315138--1315178 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1315128 GCGTTGCAAT
*
1315138 TTTCTAAAATCGCAACGCGAA
1 TTTCGAAAATCGCAACGCGAA
* *
1315159 TTTGGAAAATCGCAATGCGA
1 TTTCGAAAATCGCAACGCGA
1315179 TAGTCAAAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.37, C:0.20, G:0.20, T:0.24
Consensus pattern (21 bp):
TTTCGAAAATCGCAACGCGAA
Found at i:1315248 original size:19 final size:19
Alignment explanation
Indices: 1315224--1315260 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1315214 TGTGATACTG
*
1315224 GAGATCGCGTTGCAATTTA
1 GAGATCGCATTGCAATTTA
*
1315243 GAGATCGCATTGCGATTT
1 GAGATCGCATTGCAATTT
1315261 TGTTGGTCAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.24, C:0.16, G:0.27, T:0.32
Consensus pattern (19 bp):
GAGATCGCATTGCAATTTA
Found at i:1322752 original size:38 final size:39
Alignment explanation
Indices: 1322667--1322763 Score: 101
Period size: 38 Copynumber: 2.5 Consensus size: 39
1322657 ACTAGACTTG
* * *
1322667 AAAATATATATATCCTCCATCCGAACTCGATTCGATTTA
1 AAAATATATATAACCTCCATCCGAACTCGACTCGATCTA
* *
1322706 AAAA-ATATATAACCTTCATCCGATC-CGACTCGA-CTA
1 AAAATATATATAACCTCCATCCGAACTCGACTCGATCTA
**
1322742 AAAAGTATATATATTCTCCATC
1 AAAA-TATATATAACCTCCATC
1322764 TAATCCCGAA
Statistics
Matches: 48, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
36 6 0.12
37 7 0.15
38 31 0.65
39 4 0.08
ACGTcount: A:0.38, C:0.24, G:0.07, T:0.31
Consensus pattern (39 bp):
AAAATATATATAACCTCCATCCGAACTCGACTCGATCTA
Found at i:1324190 original size:30 final size:30
Alignment explanation
Indices: 1324154--1324212 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
1324144 AGTTATAACA
1324154 ATTTTCTTAAGGATTTTCATGAAACGACTC
1 ATTTTCTTAAGGATTTTCATGAAACGACTC
*
1324184 ATTTTCTTAAGGATTTTCATGACACGACT
1 ATTTTCTTAAGGATTTTCATGAAACGACT
1324213 GGTTCGGATA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.29, C:0.17, G:0.14, T:0.41
Consensus pattern (30 bp):
ATTTTCTTAAGGATTTTCATGAAACGACTC
Found at i:1327211 original size:12 final size:12
Alignment explanation
Indices: 1327194--1327252 Score: 100
Period size: 12 Copynumber: 4.9 Consensus size: 12
1327184 ATGAATATAA
* *
1327194 ATAAACGAGTTT
1 ATAAACGAGCTC
1327206 ATAAACGAGCTC
1 ATAAACGAGCTC
1327218 ATAAACGAGCTC
1 ATAAACGAGCTC
1327230 ATAAACGAGCTC
1 ATAAACGAGCTC
1327242 ATAAACGAGCT
1 ATAAACGAGCT
1327253 TGTTCATGAA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 45 1.00
ACGTcount: A:0.42, C:0.20, G:0.17, T:0.20
Consensus pattern (12 bp):
ATAAACGAGCTC
Found at i:1327550 original size:17 final size:18
Alignment explanation
Indices: 1327519--1327556 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
1327509 AATTTCTAGC
1327519 ATTTTTTGTGAAAATT-T
1 ATTTTTTGTGAAAATTAT
1327536 ATTTTTTGGTG-AAATTAT
1 ATTTTTT-GTGAAAATTAT
1327554 ATT
1 ATT
1327557 CTTATCCTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 12 0.63
18 7 0.37
ACGTcount: A:0.29, C:0.00, G:0.13, T:0.58
Consensus pattern (18 bp):
ATTTTTTGTGAAAATTAT
Found at i:1327653 original size:25 final size:25
Alignment explanation
Indices: 1327619--1327671 Score: 97
Period size: 25 Copynumber: 2.1 Consensus size: 25
1327609 CATTTTATCT
1327619 TTTTAAAATTAATTTTTAACAACAA
1 TTTTAAAATTAATTTTTAACAACAA
*
1327644 TTTTAAAATTAGTTTTTAACAACAA
1 TTTTAAAATTAATTTTTAACAACAA
1327669 TTT
1 TTT
1327672 CAAACAATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.43, C:0.08, G:0.02, T:0.47
Consensus pattern (25 bp):
TTTTAAAATTAATTTTTAACAACAA
Found at i:1329073 original size:19 final size:19
Alignment explanation
Indices: 1329049--1329086 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
1329039 ATTACACTCT
1329049 ATCACAAAACAACAACAAA
1 ATCACAAAACAACAACAAA
1329068 ATCACAAAACAACAACAAA
1 ATCACAAAACAACAACAAA
1329087 TTATTGTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.68, C:0.26, G:0.00, T:0.05
Consensus pattern (19 bp):
ATCACAAAACAACAACAAA
Found at i:1330459 original size:13 final size:13
Alignment explanation
Indices: 1330441--1330467 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1330431 TCAAATATAA
1330441 AATCTTAAAATTC
1 AATCTTAAAATTC
1330454 AATCTTAAAATTC
1 AATCTTAAAATTC
1330467 A
1 A
1330468 TTAACACTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.48, C:0.15, G:0.00, T:0.37
Consensus pattern (13 bp):
AATCTTAAAATTC
Found at i:1332338 original size:12 final size:12
Alignment explanation
Indices: 1332321--1332345 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1332311 CTAACATGCA
1332321 ATTTTGAAAACT
1 ATTTTGAAAACT
1332333 ATTTTGAAAACT
1 ATTTTGAAAACT
1332345 A
1 A
1332346 AGTTTGAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (12 bp):
ATTTTGAAAACT
Found at i:1356078 original size:11 final size:11
Alignment explanation
Indices: 1356062--1356121 Score: 95
Period size: 11 Copynumber: 5.5 Consensus size: 11
1356052 ACCAACAACC
1356062 ATAACAAACTA
1 ATAACAAACTA
1356073 ATAACAAACTA
1 ATAACAAACTA
1356084 ATAAC-AACTA
1 ATAACAAACTA
*
1356094 ATAACAAGCTA
1 ATAACAAACTA
1356105 ATAACAAACTA
1 ATAACAAACTA
*
1356116 TTAACA
1 ATAACA
1356122 CTCTAACATT
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
10 10 0.22
11 35 0.78
ACGTcount: A:0.60, C:0.18, G:0.02, T:0.20
Consensus pattern (11 bp):
ATAACAAACTA
Done.