Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008029.1 Hibiscus syriacus cultivar Beakdansim tig00110505_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: 3983240
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 18
Found at i:1046739 original size:13 final size:13
Alignment explanation
Indices: 1046721--1046747 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1046711 CATAAACAAT
1046721 AAAAGTACCTGCA
1 AAAAGTACCTGCA
1046734 AAAAGTACCTGCA
1 AAAAGTACCTGCA
1046747 A
1 A
1046748 GGTAATTTGG
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:0.22, G:0.15, T:0.15
Consensus pattern (13 bp):
AAAAGTACCTGCA
Found at i:1059715 original size:31 final size:31
Alignment explanation
Indices: 1059671--1059729 Score: 86
Period size: 30 Copynumber: 1.9 Consensus size: 31
1059661 CGGTCGGATT
1059671 TTTTTAAAAAAAAAATT-AGGGATCGGGTCAGA
1 TTTTT-AAAAAAAAATTCA-GGATCGGGTCAGA
1059703 TTTTT-AAAAAAAATTCAGGATCGGGTC
1 TTTTTAAAAAAAAATTCAGGATCGGGTC
1059730 GGGTTTTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
30 20 0.77
31 1 0.04
32 5 0.19
ACGTcount: A:0.41, C:0.08, G:0.20, T:0.31
Consensus pattern (31 bp):
TTTTTAAAAAAAAATTCAGGATCGGGTCAGA
Found at i:1059762 original size:32 final size:33
Alignment explanation
Indices: 1059723--1059801 Score: 124
Period size: 32 Copynumber: 2.4 Consensus size: 33
1059713 AAATTCAGGA
**
1059723 TCGGGTCGGGTTTTTTTAAGTGTGATATTCGGG
1 TCGGGTCGGGTTTTTTTAAGAATGATATTCGGG
1059756 TC-GGTCGGGTTTTTTTAAGAATGATATTCGGG
1 TCGGGTCGGGTTTTTTTAAGAATGATATTCGGG
1059788 TCGGGGTCGGGTTT
1 TC-GGGTCGGGTTT
1059802 AAGGTGAAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 3
0.89 0.04 0.06
Matches are distributed among these distances:
32 30 0.71
33 2 0.05
34 10 0.24
ACGTcount: A:0.13, C:0.10, G:0.37, T:0.41
Consensus pattern (33 bp):
TCGGGTCGGGTTTTTTTAAGAATGATATTCGGG
Found at i:1060389 original size:18 final size:18
Alignment explanation
Indices: 1060366--1060411 Score: 83
Period size: 18 Copynumber: 2.6 Consensus size: 18
1060356 ATTCCTACAG
*
1060366 ATTCCAATTCGTTCACAT
1 ATTCCAATTCATTCACAT
1060384 ATTCCAATTCATTCACAT
1 ATTCCAATTCATTCACAT
1060402 ATTCCAATTC
1 ATTCCAATTC
1060412 CCTCAGAAAC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.30, C:0.28, G:0.02, T:0.39
Consensus pattern (18 bp):
ATTCCAATTCATTCACAT
Found at i:1060550 original size:80 final size:80
Alignment explanation
Indices: 1060417--1060578 Score: 270
Period size: 80 Copynumber: 2.0 Consensus size: 80
1060407 AATTCCCTCA
* * *
1060417 GAAACATTCCAGCGAACCAAACGCCACCTAAGGGTATTCTTGTCCAAAGTGATGTGAATGTAAGA
1 GAAACATTCCAACGAACCAAACGCCACCTAAGGATATTCTTATCCAAAGTGATGTGAATGTAAGA
*
1060482 TTATCTAAGAATTTG
66 TTACCTAAGAATTTG
* *
1060497 GAAACATTCCAACGAACCAAACGCCATCTAATGATATTCTTATCCAAAGTGATGTGAATGTAAGA
1 GAAACATTCCAACGAACCAAACGCCACCTAAGGATATTCTTATCCAAAGTGATGTGAATGTAAGA
1060562 TTACCTAAGAATTTG
66 TTACCTAAGAATTTG
1060577 GA
1 GA
1060579 GGTAGTGACA
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
80 76 1.00
ACGTcount: A:0.37, C:0.19, G:0.18, T:0.27
Consensus pattern (80 bp):
GAAACATTCCAACGAACCAAACGCCACCTAAGGATATTCTTATCCAAAGTGATGTGAATGTAAGA
TTACCTAAGAATTTG
Found at i:1063449 original size:69 final size:68
Alignment explanation
Indices: 1063338--1063605 Score: 377
Period size: 69 Copynumber: 4.0 Consensus size: 68
1063328 TAGGGATTTT
1063338 TTTAGGGTAAACTACCTATTTGGTCACTTATATATTATCTAATTTATGTTTTGGTCACTCGAATT
1 TTTAGGGTAAACTACCTATTTGGTCACTTATATATTATCTAATTTATGTTTTGGTCACTCG-ATT
*
1063403 ATTG
65 ATTA
* *
1063407 TTTAGGGCAAACTACCTATTTGGTGACTTATATATTATCTAATTTATGTTTTGGTCACTCGATTA
1 TTTAGGGTAAACTACCTATTTGGTCACTTATATATTATCTAATTTATGTTTTGGTCACTCGATTA
1063472 TTA
66 TTA
** ** * * *
1063475 TTTAGGG-AAACTACCTATTTGGTCACTTATATATTATCTAA--TAT-AATTCATAAAT--ATTT
1 TTTAGGGTAAACTACCTATTTGGTCACTTATATATTATCTAATTTATGTTTTGGTCACTCGATTA
1063534 TTA
66 TTA
* *
1063537 TTTAGAGTAAACTACCTATTTGGTCACTTATATATTATCTAATTTATGTTTTGGTCACTTGATTA
1 TTTAGGGTAAACTACCTATTTGGTCACTTATATATTATCTAATTTATGTTTTGGTCACTCGATTA
1063602 TTA
66 TTA
1063605 T
1 T
1063606 ATTTTTTCAA
Statistics
Matches: 174, Mismatches: 19, Indels: 13
0.84 0.09 0.06
Matches are distributed among these distances:
62 12 0.07
63 34 0.20
64 5 0.03
65 6 0.03
66 5 0.03
67 33 0.19
68 20 0.11
69 59 0.34
ACGTcount: A:0.29, C:0.12, G:0.12, T:0.47
Consensus pattern (68 bp):
TTTAGGGTAAACTACCTATTTGGTCACTTATATATTATCTAATTTATGTTTTGGTCACTCGATTA
TTA
Found at i:1063585 original size:130 final size:134
Alignment explanation
Indices: 1063338--1063605 Score: 375
Period size: 130 Copynumber: 2.0 Consensus size: 134
1063328 TAGGGATTTT
** **
1063338 TTTAGGGTAAACTACCTATTTGGTCACTTATATATTATCTAATTTATGTTTTGGTCACTCGAATT
1 TTTAGGGTAAACTACCTATTTGGTCACTTATATATTATCTAA-TTA-GTAAT-GTCACTAAAATT
* * *
1063403 ATTGTTTAGGGCAAACTACCTATTTGGTGACTTATATATTATCTAATTTATGTTTTGGTCACTCG
63 ATTATTTAGAGCAAACTACCTATTTGGTCACTTATATATTATCTAATTTATGTTTTGGTCACTCG
1063468 ATTATTA
128 ATTATTA
*
1063475 TTTAGGG-AAACTACCTATTTGGTCACTTATATATTATCTAA-TA-TAAT-TCA-TAAATATTTT
1 TTTAGGGTAAACTACCTATTTGGTCACTTATATATTATCTAATTAGTAATGTCACTAAA-ATTAT
* *
1063535 TATTTAGAGTAAACTACCTATTTGGTCACTTATATATTATCTAATTTATGTTTTGGTCACTTGAT
65 TATTTAGAGCAAACTACCTATTTGGTCACTTATATATTATCTAATTTATGTTTTGGTCACTCGAT
1063600 TATTA
130 TATTA
1063605 T
1 T
1063606 ATTTTTTCAA
Statistics
Matches: 120, Mismatches: 10, Indels: 9
0.86 0.07 0.06
Matches are distributed among these distances:
129 2 0.02
130 73 0.61
132 2 0.02
134 2 0.02
136 34 0.28
137 7 0.06
ACGTcount: A:0.29, C:0.12, G:0.12, T:0.47
Consensus pattern (134 bp):
TTTAGGGTAAACTACCTATTTGGTCACTTATATATTATCTAATTAGTAATGTCACTAAAATTATT
ATTTAGAGCAAACTACCTATTTGGTCACTTATATATTATCTAATTTATGTTTTGGTCACTCGATT
ATTA
Found at i:1064058 original size:29 final size:28
Alignment explanation
Indices: 1064005--1064106 Score: 97
Period size: 29 Copynumber: 3.6 Consensus size: 28
1063995 ACATAAGAAT
*
1064005 GAAAAAAATGATAATAACAAT-AAATCAAA
1 GAAAAAAATAATAA-AA-AATAAAATCAAA
1064034 GAAAAAAATAATAAAGAAATAAAATCAATA
1 GAAAAAAATAATAAA-AAATAAAATCAA-A
*
1064064 -AAAATAAA-AGT-AAAAATAAAAT-AAA
1 GAAAA-AAATAATAAAAAATAAAATCAAA
1064089 GAAAAAAATAAATAAAAA
1 GAAAAAAAT-AATAAAAA
1064107 TAATAATAAA
Statistics
Matches: 62, Mismatches: 3, Indels: 17
0.76 0.04 0.21
Matches are distributed among these distances:
25 4 0.06
26 6 0.10
27 11 0.18
28 10 0.16
29 27 0.44
30 4 0.06
ACGTcount: A:0.75, C:0.03, G:0.06, T:0.16
Consensus pattern (28 bp):
GAAAAAAATAATAAAAAATAAAATCAAA
Found at i:1064071 original size:6 final size:6
Alignment explanation
Indices: 1064060--1064116 Score: 59
Period size: 6 Copynumber: 10.0 Consensus size: 6
1064050 AAATAAAATC
*
1064060 AATAAA AATAAA AGTAAA AAT-AA AATAAA GAA-AAA AAT--A AATAAA
1 AATAAA AATAAA AATAAA AATAAA AATAAA -AATAAA AATAAA AATAAA
*
1064105 AATAAT AATAAA
1 AATAAA AATAAA
1064117 TAACCTAGAA
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
4 4 0.10
5 7 0.17
6 29 0.69
7 2 0.05
ACGTcount: A:0.79, C:0.00, G:0.04, T:0.18
Consensus pattern (6 bp):
AATAAA
Found at i:1064080 original size:27 final size:27
Alignment explanation
Indices: 1064006--1064119 Score: 99
Period size: 27 Copynumber: 4.1 Consensus size: 27
1063996 CATAAGAATG
* *
1064006 AAAAAAATGATAATAACAAT-AAATCAAAG
1 AAAAAAAT-A-AATAAAAATAAAAT-AAAT
*
1064035 AAAAAAAT-AATAAAGAAATAAAATCAAT
1 AAAAAAATAAAT-AA-AAATAAAATAAAT
* *
1064063 AAAAATAA-AAGTAAAAATAAAATAAAG
1 AAAAA-AATAAATAAAAATAAAATAAAT
1064090 AAAAAAATAAATAAAAATAATAATAAAT
1 AAAAAAATAAATAAAAATAA-AATAAAT
1064118 AA
1 AA
1064120 CCTAGAAAAA
Statistics
Matches: 70, Mismatches: 8, Indels: 15
0.75 0.09 0.16
Matches are distributed among these distances:
26 5 0.07
27 29 0.41
28 20 0.29
29 16 0.23
ACGTcount: A:0.75, C:0.03, G:0.04, T:0.18
Consensus pattern (27 bp):
AAAAAAATAAATAAAAATAAAATAAAT
Found at i:1064097 original size:39 final size:39
Alignment explanation
Indices: 1064026--1064109 Score: 118
Period size: 39 Copynumber: 2.2 Consensus size: 39
1064016 TAATAACAAT
* *
1064026 AAATCAAAGAAAAAAATAATAAAGAAATAAAATCAATAA
1 AAATAAAAGAAAAAAATAATAAAGAAATAAAATAAATAA
1064065 AAATAAAAGTAAAAATAA-AATAAAGAAA-AAAATAAATAA
1 AAATAAAAG-AAAAA-AATAATAAAGAAATAAAATAAATAA
1064104 AAATAA
1 AAATAA
1064110 TAATAAATAA
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
39 24 0.59
40 15 0.37
41 2 0.05
ACGTcount: A:0.77, C:0.02, G:0.05, T:0.15
Consensus pattern (39 bp):
AAATAAAAGAAAAAAATAATAAAGAAATAAAATAAATAA
Found at i:1064114 original size:16 final size:16
Alignment explanation
Indices: 1064037--1064119 Score: 73
Period size: 16 Copynumber: 5.1 Consensus size: 16
1064027 AATCAAAGAA
*
1064037 AAAAATAATAAAGAAAT
1 AAAAATAAT-AATAAAT
1064054 -AAAATCAATAA-AAAT
1 AAAAAT-AATAATAAAT
* *
1064069 AAAAGTAAAAATAAAAT
1 AAAAATAATAAT-AAAT
*
1064086 AAAGAA-AAAAATAAAT
1 AAA-AATAATAATAAAT
1064102 AAAAATAATAATAAAT
1 AAAAATAATAATAAAT
1064118 AA
1 AA
1064120 CCTAGAAAAA
Statistics
Matches: 56, Mismatches: 4, Indels: 13
0.77 0.05 0.18
Matches are distributed among these distances:
15 10 0.18
16 29 0.52
17 16 0.29
18 1 0.02
ACGTcount: A:0.77, C:0.01, G:0.04, T:0.18
Consensus pattern (16 bp):
AAAAATAATAATAAAT
Found at i:1064149 original size:15 final size:15
Alignment explanation
Indices: 1064123--1064183 Score: 54
Period size: 15 Copynumber: 4.0 Consensus size: 15
1064113 TAAATAACCT
**
1064123 AGAAAA-ATAATACC
1 AGAAAATATAATAAA
1064137 AGAAAATATAATAAA
1 AGAAAATATAATAAA
1064152 AGAAATATATAA-AAA
1 AGAAA-ATATAATAAA
*
1064167 GAGTAAAATAAAATAAA
1 -AG-AAAATATAATAAA
1064184 GGGACAAAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
14 6 0.15
15 14 0.36
16 13 0.33
17 6 0.15
ACGTcount: A:0.70, C:0.03, G:0.08, T:0.18
Consensus pattern (15 bp):
AGAAAATATAATAAA
Found at i:1064264 original size:25 final size:26
Alignment explanation
Indices: 1064232--1064295 Score: 69
Period size: 25 Copynumber: 2.5 Consensus size: 26
1064222 TATACTAAAT
1064232 AAAT-AAATAAAAATAAGAACAAAAC
1 AAATGAAATAAAAATAAGAACAAAAC
* * * *
1064257 AAA-GAAATTAAAATATGAACAGACC
1 AAATGAAATAAAAATAAGAACAAAAC
1064282 AAATTGAAATAAAA
1 AAA-TGAAATAAAA
1064296 CAAACTTGGA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
25 23 0.74
27 8 0.26
ACGTcount: A:0.69, C:0.08, G:0.08, T:0.16
Consensus pattern (26 bp):
AAATGAAATAAAAATAAGAACAAAAC
Found at i:1066245 original size:84 final size:84
Alignment explanation
Indices: 1065978--1066727 Score: 880
Period size: 84 Copynumber: 9.0 Consensus size: 84
1065968 TAACCCTTTT
* * * * *
1065978 TGCCTTGGAGCTGAGTGTAATCGAACTCGAAGGTC-TTTGATTGGTAGATAGCCTTTCTCGACTT
1 TGCCTTGGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTG-TTGGCAGATAACCCTTCTAGCCTT
* *
1066042 AAGCTATGCTACAAATGATG
65 GAGCTATGCTGCAAATGATG
* * * *
1066062 TGCCTTTGAGTTGAGTGTAATCGAACTCGAAGGTC-TTTGTTGACAGATAACCCTTCTAGCATTG
1 TGCCTTGGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTG
* * *
1066126 AGTTATGTTGTAAATGATG
66 AGCTATGCTGCAAATGATG
* * * * *
1066145 TGTCCTT-GAACTGAGTGTAATCGAACTCGAAGGTCTTTGGTTGGCAGATATCCCTTCTCGACTT
1 TG-CCTTGGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTT
*
1066209 AAGCTATGCTGCAAATGATG
65 GAGCTATGCTGCAAATGATG
* * * * * *
1066229 TGCCTTTGAGCCGAGTGTAATCAAACTTGAAGGTC-TTTGTTGACAGATAACCCTTATAGCCTTG
1 TGCCTTGGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTG
* *
1066293 AGTTATGCTGTAAATGATG
66 AGCTATGCTGCAAATGATG
* * *
1066312 TGCCTTGGAGCTGAGCGTAATCGAACTCGAAGGTCTTTTGTTGGCAAATAACCCTTCTTGCCTTG
1 TGCCTTGGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTG
*
1066377 AGCTATGTTGCAAATGATG
66 AGCTATGCTGCAAATGATG
* * * *
1066396 TGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGCCTTTTGTTGGTAGATAACCCTTCTAGCCTTG
1 TGCCTTGGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTG
* * *
1066461 AGTTATACTACAAATGATG
66 AGCTATGCTGCAAATGATG
* * * ** * *
1066480 TG-CTTAGGAGCTGAGCGTAGTCGAACTTGAAGGTCTTTCATTGGCAGATAGCCCTTCTCGCCTT
1 TGCCTT-GGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTT
* *
1066544 GAGCTATGCTGTAAATGTTG
65 GAGCTATGCTGCAAATGATG
* * * *
1066564 TGCCTTTGATCTGAGTGTAATCGAACTCAAAGGTCTTTTGTTGGCAAATAACCCTTCTAGCCTTG
1 TGCCTTGGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTG
* *
1066629 AGTTATGCTGTAAATGATG
66 AGCTATGCTGCAAATGATG
* * * * * * *
1066648 TGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTATTGGAATATAACCCTTCTAACCTTG
1 TGCCTTGGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTG
*
1066713 AGTTATGCTGCAAAT
66 AGCTATGCTGCAAAT
1066728 AGTTTCTTTA
Statistics
Matches: 566, Mismatches: 94, Indels: 12
0.84 0.14 0.02
Matches are distributed among these distances:
83 136 0.24
84 427 0.75
85 3 0.01
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.33
Consensus pattern (84 bp):
TGCCTTGGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTG
AGCTATGCTGCAAATGATG
Found at i:1066506 original size:168 final size:167
Alignment explanation
Indices: 1065978--1066727 Score: 975
Period size: 168 Copynumber: 4.5 Consensus size: 167
1065968 TAACCCTTTT
* * * * *
1065978 TGCCTTGGAGCTGAGTGTAATCGAACTCGAAGGTC-TTTGATTGGTAGATAGCCTTTCTCGACTT
1 TGCCTTGGAGCTGAGCGTAATCGAACTCGAAGGTCTTTTG-TTGGCAGATAACCCTTCTCGCCTT
* * *
1066042 AAGCTATGCTACAAATGATGTGCCTTTGAGTTGAGTGTAATCGAACTCGAAGGTCTTTGTTGACA
65 GAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGACA
* *
1066107 GATAACCCTTCTAGCATTGAGTTATGTTGTAAATGATG
130 GATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATG
* * * * *
1066145 TGTCCTT-GAACTGAGTGTAATCGAACTCGAAGGTCTTTGGTTGGCAGATATCCCTTCTCGACTT
1 TG-CCTTGGAGCTGAGCGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCGCCTT
* * * *
1066209 AAGCTATGCTGCAAATGATGTGCCTTTGAGCCGAGTGTAATCAAACTTGAAGGTCTTTGTTGACA
65 GAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGACA
*
1066274 GATAACCCTTATAGCCTTGAGTTATGCTGTAAATGATG
130 GATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATG
* *
1066312 TGCCTTGGAGCTGAGCGTAATCGAACTCGAAGGTCTTTTGTTGGCAAATAACCCTTCTTGCCTTG
1 TGCCTTGGAGCTGAGCGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCGCCTTG
* * * * * **
1066377 AGCTATGTTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGCCTTTTGTTGGTA
66 AGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTC-TTTGTTGACA
* **
1066442 GATAACCCTTCTAGCCTTGAGTTATACTACAAATGATG
130 GATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATG
* * ** *
1066480 TG-CTTAGGAGCTGAGCGTAGTCGAACTTGAAGGTCTTTCATTGGCAGATAGCCCTTCTCGCCTT
1 TGCCTT-GGAGCTGAGCGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCGCCTT
* * * * *
1066544 GAGCTATGCTGTAAATGTTGTGCCTTTGATCTGAGTGTAATCGAACTCAAAGGTCTTTTGTTGGC
65 GAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTC-TTTGTTGAC
*
1066609 AAATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATG
129 AGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATG
* * * * * **
1066648 TGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTATTGGAATATAACCCTTCTAACCTTG
1 TGCCTTGGAGCTGAGCGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCGCCTTG
*
1066713 AGTTATGCTGCAAAT
66 AGCTATGCTGCAAAT
1066728 AGTTTCTTTA
Statistics
Matches: 511, Mismatches: 66, Indels: 11
0.87 0.11 0.02
Matches are distributed among these distances:
166 4 0.01
167 246 0.48
168 258 0.50
169 3 0.01
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.33
Consensus pattern (167 bp):
TGCCTTGGAGCTGAGCGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCGCCTTG
AGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGACAG
ATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATG
Found at i:1068058 original size:95 final size:94
Alignment explanation
Indices: 1067866--1068125 Score: 303
Period size: 95 Copynumber: 2.7 Consensus size: 94
1067856 TAGCTGAATT
* *
1067866 TATAAAGCCGGTGAGTTTAACCAATT-TCTCTAGAGGGATAACTTAATA-TCATTGTATAG-ATA
1 TATAAAGCCGG-GAGTTTAACCAATTGT-TCTAGAGGGACAAC-TAA-AGT--TT-TATTGTATA
* *
1067928 TTATAATTACCTTTATCAGGCTAGCTGAAAATTATC
59 TTATAATCACATTTATCAGGCTAGCTGAAAATTATC
*
1067964 TATAAAGCCGGGACGTTTAACCAATTGTTCTAGAGGGACAACTCAAGTTTTATTGTATATTATAA
1 TATAAAGCCGGGA-GTTTAACCAATTGTTCTAGAGGGACAACTAAAGTTTTATTGTATATTATAA
**
1068029 TCACATTTATCAGGCTAGCTGAATCTTATC
65 TCACATTTATCAGGCTAGCTGAAAATTATC
* * *
1068059 CATAAAGCCAGGGTGTTTAACCAATTGCTT-TAGAGGGACAACTAAAGCTTTATTGTATATATAT
1 TATAAAGCC-GGGAGTTTAACCAATTG-TTCTAGAGGGACAACTAAAGTTTTATTGTATAT-TAT
1068123 AAT
63 AAT
1068126 ATCATAATCT
Statistics
Matches: 144, Mismatches: 11, Indels: 16
0.84 0.06 0.09
Matches are distributed among these distances:
94 4 0.03
95 86 0.60
96 12 0.08
97 5 0.03
98 36 0.25
99 1 0.01
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.35
Consensus pattern (94 bp):
TATAAAGCCGGGAGTTTAACCAATTGTTCTAGAGGGACAACTAAAGTTTTATTGTATATTATAAT
CACATTTATCAGGCTAGCTGAAAATTATC
Found at i:1071981 original size:5 final size:5
Alignment explanation
Indices: 1071951--1072029 Score: 63
Period size: 5 Copynumber: 14.8 Consensus size: 5
1071941 CAATAAATAG
1071951 ATAAA ATCAATA A-AAA ATAAA A-AAA ATAAAA ATAAA AGTAAAA ATAAA
1 ATAAA AT-AA-A ATAAA ATAAA ATAAA AT-AAA ATAAA A-T-AAA ATAAA
* *
1071999 ATAAA ATAAAGA AAAAA ATAAA ACAAA ATAA
1 ATAAA AT-AA-A ATAAA ATAAA ATAAA ATAA
1072030 TAAATAACCT
Statistics
Matches: 61, Mismatches: 4, Indels: 18
0.73 0.05 0.22
Matches are distributed among these distances:
4 6 0.10
5 34 0.56
6 13 0.21
7 8 0.13
ACGTcount: A:0.80, C:0.03, G:0.03, T:0.15
Consensus pattern (5 bp):
ATAAA
Found at i:1071981 original size:6 final size:6
Alignment explanation
Indices: 1071959--1072021 Score: 64
Period size: 6 Copynumber: 11.2 Consensus size: 6
1071949 AGATAAAATC
* *
1071959 AATAAA AA-ATA AA-AAA AATAAA AATAAA AGTAAA AAT-AA AAT-AA
1 AATAAA AATAAA AATAAA AATAAA AATAAA AATAAA AATAAA AATAAA
1072003 AATAAA GAA-AAA AATAAA A
1 AATAAA -AATAAA AATAAA A
1072022 CAAAATAATA
Statistics
Matches: 49, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
5 20 0.41
6 27 0.55
7 2 0.04
ACGTcount: A:0.83, C:0.00, G:0.03, T:0.14
Consensus pattern (6 bp):
AATAAA
Found at i:1071987 original size:22 final size:23
Alignment explanation
Indices: 1071963--1072036 Score: 75
Period size: 22 Copynumber: 3.3 Consensus size: 23
1071953 AAAATCAATA
*
1071963 AAAAATAAAAAA-AATA-AAAAT
1 AAAAATAAAAAATAAAACAAAAT
* *
1071984 AAAAGT-AAAAATAAAATAAAAT
1 AAAAATAAAAAATAAAACAAAAT
*
1072006 AAAGA-AAAAAATAAAACAAAAT
1 AAAAATAAAAAATAAAACAAAAT
1072028 AATAAATAA
1 AA-AAATAA
1072037 CCTAAAAAAT
Statistics
Matches: 42, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
20 5 0.12
21 8 0.19
22 25 0.60
23 2 0.05
24 2 0.05
ACGTcount: A:0.81, C:0.01, G:0.03, T:0.15
Consensus pattern (23 bp):
AAAAATAAAAAATAAAACAAAAT
Found at i:1071992 original size:28 final size:29
Alignment explanation
Indices: 1071965--1072100 Score: 84
Period size: 29 Copynumber: 4.6 Consensus size: 29
1071955 AATCAATAAA
*
1071965 AAATAAAA-AAAATAAA-AATAAAAGT-AA
1 AAATAAAATAAAATAAAGAA-AAAAATAAA
1071992 AAATAAAATAAAATAAAGAAAAAAATAAA
1 AAATAAAATAAAATAAAGAAAAAAATAAA
***
1072021 ACAA-AATAAT-AAATAACCTAAAAAATAATA
1 A-AATAA-AATAAAATAAAGAAAAAAATAA-A
** * * * *
1072051 CTAGAAAATATAATAAAAGAAATATATAAA
1 AAATAAAATAAAAT-AAAGAAAAAAATAAA
1072081 AAGAGTAAAATAAAATAAAG
1 AA-A-TAAAATAAAATAAAG
1072101 GGACAAAAAG
Statistics
Matches: 82, Mismatches: 16, Indels: 18
0.71 0.14 0.16
Matches are distributed among these distances:
27 8 0.10
28 13 0.16
29 26 0.32
30 12 0.15
31 14 0.17
32 9 0.11
ACGTcount: A:0.74, C:0.03, G:0.05, T:0.18
Consensus pattern (29 bp):
AAATAAAATAAAATAAAGAAAAAAATAAA
Found at i:1071993 original size:17 final size:16
Alignment explanation
Indices: 1071963--1072036 Score: 80
Period size: 17 Copynumber: 4.5 Consensus size: 16
1071953 AAAATCAATA
1071963 AAAAATAAAA-AAAAT
1 AAAAATAAAATAAAAT
1071978 AAAAATAAAAGTAAAA-
1 AAAAATAAAA-TAAAAT
*
1071994 ATAAAATAAAATAAAGAA
1 A-AAAATAAAATAAA-AT
*
1072012 AAAAATAAAACAAAAT
1 AAAAATAAAATAAAAT
1072028 AATAAATAA
1 AA-AAATAA
1072037 CCTAAAAAAT
Statistics
Matches: 51, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
15 10 0.20
16 8 0.16
17 32 0.63
18 1 0.02
ACGTcount: A:0.81, C:0.01, G:0.03, T:0.15
Consensus pattern (16 bp):
AAAAATAAAATAAAAT
Found at i:1072026 original size:27 final size:28
Alignment explanation
Indices: 1071963--1072029 Score: 86
Period size: 27 Copynumber: 2.5 Consensus size: 28
1071953 AAAATCAATA
*
1071963 AAAAATAAAA-AAAATAAAAATAAAAGT
1 AAAAATAAAATAAAATAAAAATAAAAAT
1071990 AAAAATAAAATAAAATAAAGAA-AAAAAT
1 AAAAATAAAATAAAATAAA-AATAAAAAT
*
1072018 -AAAACAAAATAA
1 AAAAATAAAATAA
1072030 TAAATAACCT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
27 21 0.58
28 13 0.36
29 2 0.06
ACGTcount: A:0.82, C:0.01, G:0.03, T:0.13
Consensus pattern (28 bp):
AAAAATAAAATAAAATAAAAATAAAAAT
Found at i:1075057 original size:14 final size:14
Alignment explanation
Indices: 1075038--1075064 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1075028 ATTTTTTTAA
1075038 AAAAATTAAATTTT
1 AAAAATTAAATTTT
1075052 AAAAATTAAATTT
1 AAAAATTAAATTT
1075065 ATATACTTAA
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:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
AAAAATTAAATTTT
Found at i:1077629 original size:2 final size:2
Alignment explanation
Indices: 1077622--1077651 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1077612 TAATATAAGA
1077622 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1077652 TTCGTTTAGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1085700 original size:14 final size:14
Alignment explanation
Indices: 1085653--1085692 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
1085643 AAAGAAAACA
* *
1085653 AATAAGATAAAGAG
1 AATAAAATAAAAAG
1085667 AATAAAATAAAAAG
1 AATAAAATAAAAAG
*
1085681 GATAAAATAAAA
1 AATAAAATAAAA
1085693 TAAATAAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.72, C:0.00, G:0.12, T:0.15
Consensus pattern (14 bp):
AATAAAATAAAAAG
Found at i:1086768 original size:35 final size:35
Alignment explanation
Indices: 1086729--1086800 Score: 117
Period size: 35 Copynumber: 2.1 Consensus size: 35
1086719 CTAAAAAACC
1086729 CTATTTTAGACTAGTATTTAAGTCATAATCCAACT
1 CTATTTTAGACTAGTATTTAAGTCATAATCCAACT
* * *
1086764 CTATTTTAGACTAGTATTTGAGTCCTAATCCTACT
1 CTATTTTAGACTAGTATTTAAGTCATAATCCAACT
1086799 CT
1 CT
1086801 TCTTTTTTGG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.29, C:0.19, G:0.10, T:0.42
Consensus pattern (35 bp):
CTATTTTAGACTAGTATTTAAGTCATAATCCAACT
Found at i:1087465 original size:106 final size:105
Alignment explanation
Indices: 1087279--1088122 Score: 942
Period size: 106 Copynumber: 8.0 Consensus size: 105
1087269 TGTATTGTTC
* * * * *
1087279 CGAGTCCAATATCCTTCGCCGTGAAGTTGAAATTGGCTCTGGAACTGGAAAATTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAAATTGGGAAATTGTTTGTTGACA
* * * ** *
1087344 GCCAACCGCCCCTTCACTGTGAAGTTGAGCTTGTGCTGTCT
66 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTG-TGTCT
* * * * * *
1087385 TGAGTCTAATATCCTTCGATGTGAAGTTGAAATTGACCCTTAAATTAGGAAATTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAAATTGGGAAATTGTTTGTTGACA
*
1087450 ACCAGCCGTCCCTTCATTGTGAAGTTGAACTTGTGTAGTCT
66 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGT-GTCT
* *
1087491 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTATTTGTTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAAATTGGGAAATTGTTTGTTGACA
* *
1087556 ACCAGCCGCCCCTTCATTGTGAAGTTGAACTTGTG-GTCT
66 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTGTCT
* * * * * * **
1087595 CGAGTCCAATATTCTTCGATGTAAAGTTGAAATTGACCCTGAAATTAGGAAATTGTTTATTGGGA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAAATTGGGAAATTGTTTGTTGACA
* * * * *
1087660 ACCAGCTGTGCCTTTGTTGTAAAGTTGAACTTGTGTCATCT
66 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGT-GTCT
*
1087701 CGAGTCCAATATCCTTCGC--T--A-TTG-----G-CTCTGAAATTGGGAGATTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAAATTGGGAAATTGTTTGTTGACA
* *
1087755 ACCAGCCATCCATTCGTTGTGAAGTTGAACTTGTGTTGTCT
66 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTG-TGTCT
** *
1087796 TAAGTCCAATATCCTTCGCTATGAAGTTGAAATTGACTCTGAAATTGGGAAATTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAAATTGGGAAATTGTTTGTTGACA
*
1087861 ACCAGTCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTC-
66 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTG-TGTCT
* ** * *
1087901 CTGAGTCCAACATCCTTCTATGTGAAGTTGAAATTGGCTCTAAAATTGGGAAATTGTTTGTTGAC
1 C-GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAAATTGGGAAATTGTTTGTTGAC
* ** *
1087966 AATCAGCTATCCCTTCGTTGTGAAGTTGAACTTGTGTTATCT
65 AACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTG-TGTCT
* * * * *
1088008 CGAATCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAATGAAACT-GAAAAGTGGTTTGT
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTC----TGAAATTGGGAAA-TTGTTTGT
* * *
1088072 TGACAACCAACCGTTCATTCGTTGTGAAGTTGAACTTGTGTTGTCT
61 TGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTG-TGTCT
1088118 CGAGT
1 CGAGT
1088123 GGCGCGATAT
Statistics
Matches: 624, Mismatches: 92, Indels: 40
0.83 0.12 0.05
Matches are distributed among these distances:
95 72 0.12
96 2 0.00
97 1 0.00
99 1 0.00
100 3 0.00
101 3 0.00
102 1 0.00
104 89 0.14
105 2 0.00
106 390 0.62
107 1 0.00
109 4 0.01
110 55 0.09
ACGTcount: A:0.25, C:0.18, G:0.22, T:0.35
Consensus pattern (105 bp):
CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAAATTGGGAAATTGTTTGTTGACA
ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTGTCT
Found at i:1087841 original size:305 final size:306
Alignment explanation
Indices: 1087426--1088027 Score: 884
Period size: 305 Copynumber: 2.0 Consensus size: 306
1087416 ATTGACCCTT
* *
1087426 AAATTAGGAAATTGTTTGTTGACAACCAGCCGTCCCTTCATTGTGAAGTTGAACTTGTGTAGTCT
1 AAATTAGGAAATTGTTTGTTGACAACCAGCCATCCATTCATTGTGAAGTTGAACTTGTGTAGTCT
* * *
1087491 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTATTTGTTGACA
66 CAAGTCCAATATCCTTCGCTATGAAGTTGAAATTGACTCTGAAATTGGGAAATTATTTGTTGACA
* *
1087556 ACCAGCCGCCCCTTCATTGTGAAGTTGAACTTGTG-GT-CTCGAGTCCAATATTCTTCGATGTAA
131 ACCAGCCGCCCCTTCATTGTGAAGTTGAACTTGTGTGTCCT-GAGTCCAACATCCTTCGATGTAA
* ** * * *
1087619 AGTTGAAATTGACCCTGAAATTAGGAAATTGTTTATTGGGAACCAGCTGTGCCTTTGTTGTAAAG
195 AGTTGAAATTGACCCTAAAATTAGGAAATTGTTTATTGACAACCAGCTATCCCTTCGTTGTAAAG
*
1087684 TTGAACTTGTGTCATCTCGAGTCCAATATCCTTCGCTATTGGCTCTG
260 TTGAACTTGTGTCATCTCGAATCCAATATCCTTCGCTATTGGCTCTG
* * * *
1087731 AAATTGGGAGATTGTTTGTTGACAACCAGCCATCCATTCGTTGTGAAGTTGAACTTGTGTTGTCT
1 AAATTAGGAAATTGTTTGTTGACAACCAGCCATCCATTCATTGTGAAGTTGAACTTGTGTAGTCT
* *
1087796 TAAGTCCAATATCCTTCGCTATGAAGTTGAAATTGACTCTGAAATTGGGAAATTGTTTGTTGACA
66 CAAGTCCAATATCCTTCGCTATGAAGTTGAAATTGACTCTGAAATTGGGAAATTATTTGTTGACA
* * * * *
1087861 ACCAGTCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCCTGAGTCCAACATCCTTCTATGTGA
131 ACCAGCCGCCCCTTCATTGTGAAGTTGAACTTGTG-TGTCCTGAGTCCAACATCCTTCGATGTAA
* * * * * *
1087926 AGTTGAAATTGGCTCTAAAATTGGGAAATTGTTTGTTGACAATCAGCTATCCCTTCGTTGTGAAG
195 AGTTGAAATTGACCCTAAAATTAGGAAATTGTTTATTGACAACCAGCTATCCCTTCGTTGTAAAG
*
1087991 TTGAACTTGTGTTATCTCGAATCCAATATCCTTCGCT
260 TTGAACTTGTGTCATCTCGAATCCAATATCCTTCGCT
1088028 GTGAAGTTGA
Statistics
Matches: 262, Mismatches: 32, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
305 151 0.58
307 109 0.42
308 2 0.01
ACGTcount: A:0.25, C:0.18, G:0.22, T:0.35
Consensus pattern (306 bp):
AAATTAGGAAATTGTTTGTTGACAACCAGCCATCCATTCATTGTGAAGTTGAACTTGTGTAGTCT
CAAGTCCAATATCCTTCGCTATGAAGTTGAAATTGACTCTGAAATTGGGAAATTATTTGTTGACA
ACCAGCCGCCCCTTCATTGTGAAGTTGAACTTGTGTGTCCTGAGTCCAACATCCTTCGATGTAAA
GTTGAAATTGACCCTAAAATTAGGAAATTGTTTATTGACAACCAGCTATCCCTTCGTTGTAAAGT
TGAACTTGTGTCATCTCGAATCCAATATCCTTCGCTATTGGCTCTG
Found at i:1089108 original size:16 final size:16
Alignment explanation
Indices: 1089069--1089110 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
1089059 TGAACCCACC
1089069 TTATTTTGTTCTTTTTG
1 TTATTTT-TTCTTTTTG
*
1089086 TTCTTTTTTCTCTTTT-
1 TTATTTTTTCT-TTTTG
1089102 TTATTTTTT
1 TTATTTTTT
1089111 TCAATTTAGG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 12 0.55
17 10 0.45
ACGTcount: A:0.05, C:0.10, G:0.05, T:0.81
Consensus pattern (16 bp):
TTATTTTTTCTTTTTG
Found at i:1096983 original size:2 final size:2
Alignment explanation
Indices: 1096976--1097002 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1096966 TATTAAAGAA
1096976 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1097003 AAATATAGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1097088 original size:17 final size:18
Alignment explanation
Indices: 1097055--1097090 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1097045 ATATATACGT
*
1097055 ATAATAATAACATGAATA
1 ATAAAAATAACATGAATA
1097073 ATAAAAATAA-ATGAATA
1 ATAAAAATAACATGAATA
1097090 A
1 A
1097091 AATATCCATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.67, C:0.03, G:0.06, T:0.25
Consensus pattern (18 bp):
ATAAAAATAACATGAATA
Found at i:1097508 original size:35 final size:35
Alignment explanation
Indices: 1097469--1097540 Score: 126
Period size: 35 Copynumber: 2.1 Consensus size: 35
1097459 CTAAAAAACC
*
1097469 CTATTTTAGACTAGTATTTGAGTTCTAATCCAACT
1 CTATTTTAGACTAGTATTTGAGTCCTAATCCAACT
*
1097504 CTATTTTAGACTAGTATTTGAGTCCTAATCCTACT
1 CTATTTTAGACTAGTATTTGAGTCCTAATCCAACT
1097539 CT
1 CT
1097541 TCTTTTTTGG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.26, C:0.19, G:0.11, T:0.43
Consensus pattern (35 bp):
CTATTTTAGACTAGTATTTGAGTCCTAATCCAACT
Found at i:1099908 original size:19 final size:20
Alignment explanation
Indices: 1099870--1099920 Score: 63
Period size: 19 Copynumber: 2.7 Consensus size: 20
1099860 TTAAGCATAG
*
1099870 TTTAATATC-A-TAATATTA
1 TTTAATATCAATTAATAATA
*
1099888 TTTCATA-CAATTAATAATA
1 TTTAATATCAATTAATAATA
1099907 TTTAATATCAATTA
1 TTTAATATCAATTA
1099921 TATTAAGAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
17 1 0.04
18 7 0.26
19 13 0.48
20 6 0.22
ACGTcount: A:0.45, C:0.08, G:0.00, T:0.47
Consensus pattern (20 bp):
TTTAATATCAATTAATAATA
Found at i:1101181 original size:22 final size:22
Alignment explanation
Indices: 1101153--1101208 Score: 85
Period size: 22 Copynumber: 2.5 Consensus size: 22
1101143 TACGCTGTCT
*
1101153 TTCGGGACATATACAGAGGTCC
1 TTCGGGACAAATACAGAGGTCC
**
1101175 TTCGGGACAAATACATTGGTCC
1 TTCGGGACAAATACAGAGGTCC
1101197 TTCGGGACAAAT
1 TTCGGGACAAAT
1101209 TTCACATGCC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.29, C:0.21, G:0.25, T:0.25
Consensus pattern (22 bp):
TTCGGGACAAATACAGAGGTCC
Found at i:1102100 original size:59 final size:56
Alignment explanation
Indices: 1102028--1102142 Score: 176
Period size: 59 Copynumber: 2.0 Consensus size: 56
1102018 TTGAGGTGTT
* *
1102028 ACACATAAGGTTGTGCCCACCATCTGCACTAGTTATACTTTAGTGCAATCCCGAATATG
1 ACACATAAGGTTGTGCCCACCATATGCACTA---ATACTTTAGTGCAATCCCAAATATG
*
1102087 ACACATAAGGTTGTGCCCACCATATGCACTAATACTTTAGTGTAATCCCAAATATG
1 ACACATAAGGTTGTGCCCACCATATGCACTAATACTTTAGTGCAATCCCAAATATG
1102143 CAGCCTGCTG
Statistics
Matches: 53, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
56 23 0.43
59 30 0.57
ACGTcount: A:0.31, C:0.24, G:0.16, T:0.29
Consensus pattern (56 bp):
ACACATAAGGTTGTGCCCACCATATGCACTAATACTTTAGTGCAATCCCAAATATG
Found at i:1103443 original size:49 final size:49
Alignment explanation
Indices: 1103367--1103465 Score: 180
Period size: 49 Copynumber: 2.0 Consensus size: 49
1103357 TTCCCGATGC
*
1103367 TTATTCAATACAATTTCCATGTTACAACATAAATGTTGACCTTAACACT
1 TTATTCAATACAATTTCCATGTCACAACATAAATGTTGACCTTAACACT
*
1103416 TTATTCGATACAATTTCCATGTCACAACATAAATGTTGACCTTAACACT
1 TTATTCAATACAATTTCCATGTCACAACATAAATGTTGACCTTAACACT
1103465 T
1 T
1103466 CCAATTAACC
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 48 1.00
ACGTcount: A:0.35, C:0.21, G:0.07, T:0.36
Consensus pattern (49 bp):
TTATTCAATACAATTTCCATGTCACAACATAAATGTTGACCTTAACACT
Found at i:1103896 original size:30 final size:30
Alignment explanation
Indices: 1103840--1103896 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
1103830 CAACCATTCA
* *
1103840 CAACTTTCCAAAATTGACAAATTGGTCCCT
1 CAACTTTCAAAAATTGACAAAATGGTCCCT
*
1103870 CAACTTTTCAAAAATT-ATAAAATGGTC
1 CAAC-TTTCAAAAATTGACAAAATGGTC
1103897 TTAAAATTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
30 13 0.57
31 10 0.43
ACGTcount: A:0.39, C:0.21, G:0.09, T:0.32
Consensus pattern (30 bp):
CAACTTTCAAAAATTGACAAAATGGTCCCT
Found at i:1105621 original size:17 final size:15
Alignment explanation
Indices: 1105592--1105630 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
1105582 CGTCTAATCC
1105592 CTTAAATCCCTAAACT
1 CTTAAATCCCT-AACT
*
1105608 CTTATAATCTCTAACT
1 CTTA-AATCCCTAACT
1105624 CTTAAAT
1 CTTAAAT
1105631 TCACTCATCA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 3 0.14
16 12 0.57
17 6 0.29
ACGTcount: A:0.36, C:0.26, G:0.00, T:0.38
Consensus pattern (15 bp):
CTTAAATCCCTAACT
Found at i:1109056 original size:36 final size:36
Alignment explanation
Indices: 1109002--1109074 Score: 112
Period size: 36 Copynumber: 2.0 Consensus size: 36
1108992 GGCAAAGAGT
1109002 GCAGGTCTCCCAGGACATGTTCTTCCTCCTACAAAC
1 GCAGGTCTCCCAGGACATGTTCTTCCTCCTACAAAC
* *
1109038 GCAGGTCTCTC-GGAACATGTTCTTCCTCCTCCAAAC
1 GCAGGTCTCCCAGG-ACATGTTCTTCCTCCTACAAAC
1109074 G
1 G
1109075 TAAGACACAG
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
35 2 0.06
36 32 0.94
ACGTcount: A:0.21, C:0.36, G:0.18, T:0.26
Consensus pattern (36 bp):
GCAGGTCTCCCAGGACATGTTCTTCCTCCTACAAAC
Found at i:1114300 original size:22 final size:22
Alignment explanation
Indices: 1114274--1114384 Score: 160
Period size: 22 Copynumber: 5.3 Consensus size: 22
1114264 CTAAATGGAA
1114274 CGTTCAGCGCTGAATGGTGAAC
1 CGTTCAGCGCTGAATGGTGAAC
* *
1114296 CGTTCAGCTCTGAAAGGTGAAC
1 CGTTCAGCGCTGAATGGTGAAC
*
1114318 CGTTCAGCGCTGAAAGGTGAAC
1 CGTTCAGCGCTGAATGGTGAAC
1114340 CGTT-----CTGAATGGTGAAC
1 CGTTCAGCGCTGAATGGTGAAC
1114357 CGTTCAGCGCTGAATGGTGAAC
1 CGTTCAGCGCTGAATGGTGAAC
1114379 CGTTCA
1 CGTTCA
1114385 ACATTCAGCG
Statistics
Matches: 80, Mismatches: 4, Indels: 10
0.85 0.04 0.11
Matches are distributed among these distances:
17 16 0.20
22 64 0.80
ACGTcount: A:0.24, C:0.23, G:0.30, T:0.23
Consensus pattern (22 bp):
CGTTCAGCGCTGAATGGTGAAC
Found at i:1114353 original size:17 final size:17
Alignment explanation
Indices: 1114304--1114361 Score: 62
Period size: 17 Copynumber: 3.1 Consensus size: 17
1114294 ACCGTTCAGC
1114304 TCTGAAAGGTGAACCGT
1 TCTGAAAGGTGAACCGT
1114321 TCAGCGCTGAAAGGTGAACCGT
1 T-----CTGAAAGGTGAACCGT
*
1114343 TCTGAATGGTGAACCGT
1 TCTGAAAGGTGAACCGT
1114360 TC
1 TC
1114362 AGCGCTGAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
17 18 0.51
22 17 0.49
ACGTcount: A:0.26, C:0.21, G:0.29, T:0.24
Consensus pattern (17 bp):
TCTGAAAGGTGAACCGT
Found at i:1114358 original size:39 final size:39
Alignment explanation
Indices: 1114274--1114383 Score: 157
Period size: 39 Copynumber: 2.7 Consensus size: 39
1114264 CTAAATGGAA
1114274 CGTTCAGCGCTGAATGGTGAACCGTTCAGCTCTGAAAGGTGAAC
1 CGTTCAGCGCTGAATGGTGAACCG-T----TCTGAAAGGTGAAC
* *
1114318 CGTTCAGCGCTGAAAGGTGAACCGTTCTGAATGGTGAAC
1 CGTTCAGCGCTGAATGGTGAACCGTTCTGAAAGGTGAAC
1114357 CGTTCAGCGCTGAATGGTGAACCGTTC
1 CGTTCAGCGCTGAATGGTGAACCGTTC
1114384 AACATTCAGC
Statistics
Matches: 63, Mismatches: 3, Indels: 5
0.89 0.04 0.07
Matches are distributed among these distances:
39 39 0.62
43 1 0.02
44 23 0.37
ACGTcount: A:0.24, C:0.23, G:0.30, T:0.24
Consensus pattern (39 bp):
CGTTCAGCGCTGAATGGTGAACCGTTCTGAAAGGTGAAC
Found at i:1115367 original size:2 final size:2
Alignment explanation
Indices: 1115360--1115387 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1115350 TGCTCCCCAG
1115360 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1115388 TGCAATTTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1116174 original size:17 final size:17
Alignment explanation
Indices: 1116154--1116195 Score: 84
Period size: 17 Copynumber: 2.5 Consensus size: 17
1116144 AAGCGTGAGC
1116154 CAGTAACAAGTGAACAA
1 CAGTAACAAGTGAACAA
1116171 CAGTAACAAGTGAACAA
1 CAGTAACAAGTGAACAA
1116188 CAGTAACA
1 CAGTAACA
1116196 GAATTTCTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.52, C:0.19, G:0.17, T:0.12
Consensus pattern (17 bp):
CAGTAACAAGTGAACAA
Found at i:1119017 original size:12 final size:12
Alignment explanation
Indices: 1119002--1119029 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
1118992 AGAACTTGAA
1119002 GATCTCGATGAT
1 GATCTCGATGAT
1119014 GATCTCGATGAT
1 GATCTCGATGAT
1119026 GATC
1 GATC
1119030 GATTCCTTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.32
Consensus pattern (12 bp):
GATCTCGATGAT
Found at i:1135709 original size:81 final size:81
Alignment explanation
Indices: 1135569--1135725 Score: 242
Period size: 81 Copynumber: 1.9 Consensus size: 81
1135559 GTCTCTTGCA
* * * * *
1135569 CAACTGGCTCGGTAGCTTCCTGCTCTACACCTCTGTGAGAGCTTGTCGATTCGCCATTTCGTGTG
1 CAACAGGCTCAGTAACTTCATGCTCTACACCTCTGTGAGAGCTTGTCGATCCGCCATTTCGTGTG
*
1135634 CGAACCATTCTCGGTG
66 CAAACCATTCTCGGTG
* *
1135650 CAACAGGCTCAGTAACTTCATGCTCTACACCTCTGTGAGAGCTTGTTGCTCCGCCATTTCGTGTG
1 CAACAGGCTCAGTAACTTCATGCTCTACACCTCTGTGAGAGCTTGTCGATCCGCCATTTCGTGTG
1135715 CAAACCATTCT
66 CAAACCATTCT
1135726 TTGCAACTCG
Statistics
Matches: 68, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
81 68 1.00
ACGTcount: A:0.18, C:0.30, G:0.22, T:0.31
Consensus pattern (81 bp):
CAACAGGCTCAGTAACTTCATGCTCTACACCTCTGTGAGAGCTTGTCGATCCGCCATTTCGTGTG
CAAACCATTCTCGGTG
Found at i:1135901 original size:55 final size:55
Alignment explanation
Indices: 1135842--1135976 Score: 218
Period size: 55 Copynumber: 2.5 Consensus size: 55
1135832 TAGAATTAAC
* *
1135842 GATTGAGCACCTCTGTGCTTCAATCGAGAGCTGACACCTCTGTGTAGCCAA-AAGT
1 GATTGAGCACCTCTGTGCTTCAATCGAGAACTGACACCTCTGTGCAGCCAACAA-T
*
1135897 GATTGAGCACCTCTGTGCTTCAATCGAGAACTGACACCTCTGTGCAGCCAACTAT
1 GATTGAGCACCTCTGTGCTTCAATCGAGAACTGACACCTCTGTGCAGCCAACAAT
*
1135952 GACTGAGCACCTCTGTGCTTCAATC
1 GATTGAGCACCTCTGTGCTTCAATC
1135977 TAAATTCTGG
Statistics
Matches: 75, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
55 74 0.99
56 1 0.01
ACGTcount: A:0.24, C:0.28, G:0.21, T:0.26
Consensus pattern (55 bp):
GATTGAGCACCTCTGTGCTTCAATCGAGAACTGACACCTCTGTGCAGCCAACAAT
Found at i:1135940 original size:27 final size:27
Alignment explanation
Indices: 1135845--1135976 Score: 110
Period size: 27 Copynumber: 4.8 Consensus size: 27
1135835 AATTAACGAT
1135845 TGAGCACCTCTGTGCTTCAATCGAGAGC
1 TGAGCACCTCTGTGCTTCAATCGAGA-C
* ** * *
1135873 TGA-CACCTCTGTG-TAGCCAAAAGTGAT
1 TGAGCACCTCTGTGCT--TCAATCGAGAC
1135900 TGAGCACCTCTGTGCTTCAATCGAGAAC
1 TGAGCACCTCTGTGCTTCAATCGAG-AC
** *
1135928 TGA-CACCTCTGTGCAGCCAA-CTATGAC
1 TGAGCACCTCTGTGC-TTCAATCGA-GAC
1135955 TGAGCACCTCTGTGCTTCAATC
1 TGAGCACCTCTGTGCTTCAATC
1135977 TAAATTCTGG
Statistics
Matches: 80, Mismatches: 15, Indels: 18
0.71 0.13 0.16
Matches are distributed among these distances:
26 1 0.01
27 39 0.49
28 39 0.49
29 1 0.01
ACGTcount: A:0.24, C:0.29, G:0.21, T:0.26
Consensus pattern (27 bp):
TGAGCACCTCTGTGCTTCAATCGAGAC
Found at i:1142733 original size:41 final size:41
Alignment explanation
Indices: 1142681--1143053 Score: 184
Period size: 41 Copynumber: 9.3 Consensus size: 41
1142671 TAGAGGTGTT
* * *
1142681 TTTTTAT-CAAACGCTGCAAAAGAATCTTACTTTAGTGGCA
1 TTTTTATACAAACGCTGCAAAAGACTCGTACTTTAGTGGCG
* * * * *
1142721 TTTGTATACAAACGCCGCTAAAGACTCAG-AATTTCGTGGCG
1 TTTTTATACAAACGCTGCAAAAGACTC-GTACTTTAGTGGCG
* * *
1142762 TTTGTATAAAAACG-TAGCTATAA-ACTCGTACTTTAGTGGCG
1 TTTTTATACAAACGCT-GC-AAAAGACTCGTACTTTAGTGGCG
* *
1142803 TTTTTAT-CAAACG-TCGCTATAA-ACTCGTACTTTAGTGGCA
1 TTTTTATACAAACGCT-GC-AAAAGACTCGTACTTTAGTGGCG
* * * * * * *
1142843 TTTTTATACAATCTCCGCTATAGAATCGTACTTTAGTTGCG
1 TTTTTATACAAACGCTGCAAAAGACTCGTACTTTAGTGGCG
* * * * *
1142884 TTTTTATACAAACACCGCTATAGAATCG-----TA---GCG
1 TTTTTATACAAACGCTGCAAAAGACTCGTACTTTAGTGGCG
** * * * * **
1142917 TTTTTATACAAGTGCCGCTATAGACTCGTACTTCAGTGGTA
1 TTTTTATACAAACGCTGCAAAAGACTCGTACTTTAGTGGCG
* * * * * * *
1142958 TTTTTATACAAATGCCGCTATAA-ACTCATATTTTAGTGACA
1 TTTTTATACAAACGCTGC-AAAAGACTCGTACTTTAGTGGCG
* * * *
1142999 TTTTTATATAAACGCTGCTATAGACTTGTACTTTAGTGGCG
1 TTTTTATACAAACGCTGCAAAAGACTCGTACTTTAGTGGCG
1143040 TTTTTATACAAACG
1 TTTTTATACAAACG
1143054 TCGTAATAGT
Statistics
Matches: 258, Mismatches: 57, Indels: 35
0.74 0.16 0.10
Matches are distributed among these distances:
33 27 0.10
36 2 0.01
38 1 0.00
40 46 0.18
41 179 0.69
42 3 0.01
ACGTcount: A:0.29, C:0.18, G:0.16, T:0.36
Consensus pattern (41 bp):
TTTTTATACAAACGCTGCAAAAGACTCGTACTTTAGTGGCG
Found at i:1142923 original size:33 final size:33
Alignment explanation
Indices: 1142881--1142946 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
1142871 TACTTTAGTT
1142881 GCGTTTTTATACAAACACCGCTATAGAATCGTA
1 GCGTTTTTATACAAACACCGCTATAGAATCGTA
*** *
1142914 GCGTTTTTATACAAGTGCCGCTATAGACTCGTA
1 GCGTTTTTATACAAACACCGCTATAGAATCGTA
1142947 CTTCAGTGGT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Consensus pattern (33 bp):
GCGTTTTTATACAAACACCGCTATAGAATCGTA
Found at i:1142976 original size:115 final size:114
Alignment explanation
Indices: 1142800--1143022 Score: 272
Period size: 115 Copynumber: 1.9 Consensus size: 114
1142790 TACTTTAGTG
* * *
1142800 GCGTTTTTATCAAACGTCGCTATAAACTCGTACTTTAGTGGCATTTTTATACAATCTCCGCTATA
1 GCGTTTTTATCAAACGCCGCTATAAACTCGTACTTCAGTGGCATTTTTATACAATCGCCGCTATA
* *
1142865 GAA-TCGTACTTTAGTTG-CGTTTTTATACAAACACCGCTATAGAATCGTA
66 -AACTCATACTTTAG-TGACATTTTTATACAAACACCGCTATAGAATCGTA
** * *
1142914 GCGTTTTTATACAAGTGCCGCTATAGACTCGTACTTCAGTGGTATTTTTATACAAAT-GCCGCTA
1 GCGTTTTTAT-CAAACGCCGCTATAAACTCGTACTTCAGTGGCATTTTTATAC-AATCGCCGCTA
* * * *
1142978 TAAACTCATATTTTAGTGACATTTTTATATAAACGCTGCTATAGA
64 TAAACTCATACTTTAGTGACATTTTTATACAAACACCGCTATAGA
1143023 CTTGTACTTT
Statistics
Matches: 92, Mismatches: 13, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
114 14 0.15
115 75 0.82
116 3 0.03
ACGTcount: A:0.29, C:0.19, G:0.15, T:0.37
Consensus pattern (114 bp):
GCGTTTTTATCAAACGCCGCTATAAACTCGTACTTCAGTGGCATTTTTATACAATCGCCGCTATA
AACTCATACTTTAGTGACATTTTTATACAAACACCGCTATAGAATCGTA
Found at i:1143070 original size:41 final size:40
Alignment explanation
Indices: 1143025--1143126 Score: 125
Period size: 42 Copynumber: 2.5 Consensus size: 40
1143015 GCTATAGACT
*
1143025 TGTACTTTAGTGGCGTTTTTATACAAACGTCGTAATAGTCA
1 TGTACTTTAGTGGCGTTTTTA-ACAAACGACGTAATAGTCA
* ** *
1143066 TGTACCTTAGTTTCAGTTTTGTAATAAACGACGTAATAGTCA
1 TGTACTTTAGTGGC-GTTTT-TAACAAACGACGTAATAGTCA
1143108 TGTACTTTAGTGG-GTTTTT
1 TGTACTTTAGTGGCGTTTTT
1143127 TTTTGCAATA
Statistics
Matches: 51, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
39 1 0.02
40 5 0.10
41 11 0.22
42 32 0.63
43 2 0.04
ACGTcount: A:0.25, C:0.13, G:0.20, T:0.42
Consensus pattern (40 bp):
TGTACTTTAGTGGCGTTTTTAACAAACGACGTAATAGTCA
Found at i:1145154 original size:16 final size:15
Alignment explanation
Indices: 1145133--1145164 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
1145123 AACAGAATTT
1145133 TAGGTAAAATAACAAA
1 TAGGTAAAATAA-AAA
1145149 TAGGTAAAATAAAAA
1 TAGGTAAAATAAAAA
1145164 T
1 T
1145165 TTTCCCCTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.62, C:0.03, G:0.12, T:0.22
Consensus pattern (15 bp):
TAGGTAAAATAAAAA
Found at i:1149825 original size:3 final size:3
Alignment explanation
Indices: 1149817--1149855 Score: 60
Period size: 3 Copynumber: 13.0 Consensus size: 3
1149807 TATATACTCT
* *
1149817 TGA TGA TGA TGG TAA TGA TGA TGA TGA TGA TGA TGA TGA
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
1149856 GAGTCATAAC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
TGA
Found at i:1149977 original size:13 final size:13
Alignment explanation
Indices: 1149959--1149984 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1149949 ACATTTCATT
1149959 ATTTTTTTATTTA
1 ATTTTTTTATTTA
1149972 ATTTTTTTATTTA
1 ATTTTTTTATTTA
1149985 CTTGCAATTG
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:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (13 bp):
ATTTTTTTATTTA
Found at i:1150103 original size:25 final size:25
Alignment explanation
Indices: 1150039--1150104 Score: 64
Period size: 25 Copynumber: 2.6 Consensus size: 25
1150029 TAATTTATTT
1150039 TGTTTGTTAA-TTTTTTATTACTTAG
1 TGTTT-TTAATTTTTTTATTACTTAG
** * *
1150064 T-TGTTCAAATGTTTTTATTATTTAG
1 TGT-TTTTAATTTTTTTATTACTTAG
1150089 TGTTTTTAATTTTTTT
1 TGTTTTTAATTTTTTT
1150105 TTGTTATATC
Statistics
Matches: 31, Mismatches: 7, Indels: 6
0.70 0.16 0.14
Matches are distributed among these distances:
24 3 0.10
25 27 0.87
26 1 0.03
ACGTcount: A:0.20, C:0.03, G:0.11, T:0.67
Consensus pattern (25 bp):
TGTTTTTAATTTTTTTATTACTTAG
Found at i:1153364 original size:21 final size:18
Alignment explanation
Indices: 1153340--1153378 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 18
1153330 TTTTTTTCGA
1153340 ATAATCATATATAAAATAAAT
1 ATAAT-ATAT-TAAAA-AAAT
1153361 ATAATATATTAAAAAAAT
1 ATAATATATTAAAAAAAT
1153379 TACCTTACAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 4 0.22
19 5 0.28
20 4 0.22
21 5 0.28
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (18 bp):
ATAATATATTAAAAAAAT
Found at i:1154036 original size:12 final size:12
Alignment explanation
Indices: 1154019--1154052 Score: 68
Period size: 12 Copynumber: 2.8 Consensus size: 12
1154009 GTATTGCAAA
1154019 TTCGCGTTGCAT
1 TTCGCGTTGCAT
1154031 TTCGCGTTGCAT
1 TTCGCGTTGCAT
1154043 TTCGCGTTGC
1 TTCGCGTTGC
1154053 GATAGTTGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.06, C:0.26, G:0.26, T:0.41
Consensus pattern (12 bp):
TTCGCGTTGCAT
Found at i:1154114 original size:41 final size:41
Alignment explanation
Indices: 1154065--1154261 Score: 358
Period size: 41 Copynumber: 4.8 Consensus size: 41
1154055 TAGTTGAAAA
* *
1154065 TCGCGTTGCGATAGTCTACAGTGTTGTTGCTATTTTCCATT
1 TCGCGTTGCGATAGTCTACAGTGTCGTTGCGATTTTCCATT
1154106 TCGCGTTGCGATAGTCTACAGTGTCGTTGCGATTTTCCATT
1 TCGCGTTGCGATAGTCTACAGTGTCGTTGCGATTTTCCATT
* *
1154147 TCGCGTTGCGATAGTGTACAGTGTCGTTGCGATTTTCCATC
1 TCGCGTTGCGATAGTCTACAGTGTCGTTGCGATTTTCCATT
1154188 TCGCGTTGCGATAGTCTACAGTGTCGTTGCGATTTTCCATT
1 TCGCGTTGCGATAGTCTACAGTGTCGTTGCGATTTTCCATT
1154229 TCGCGTTGCGATAGTCTACAGTGTCGTTGCGAT
1 TCGCGTTGCGATAGTCTACAGTGTCGTTGCGAT
1154262 AGTCTACAGT
Statistics
Matches: 150, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 150 1.00
ACGTcount: A:0.15, C:0.21, G:0.25, T:0.39
Consensus pattern (41 bp):
TCGCGTTGCGATAGTCTACAGTGTCGTTGCGATTTTCCATT
Found at i:1154134 original size:21 final size:21
Alignment explanation
Indices: 1154109--1154271 Score: 119
Period size: 21 Copynumber: 7.9 Consensus size: 21
1154099 TTCCATTTCG
1154109 CGTTGCGATAGTCTACAGTGT
1 CGTTGCGATAGTCTACAGTGT
* * *
1154130 CGTTGCGAT--TTTCCA-TTT
1 CGTTGCGATAGTCTACAGTGT
*
1154148 CGCGTTGCGATAGTGTACAGTGT
1 --CGTTGCGATAGTCTACAGTGT
* * *
1154171 CGTTGCGAT--TTTCCA-TCT
1 CGTTGCGATAGTCTACAGTGT
1154189 CGCGTTGCGATAGTCTACAGTGT
1 --CGTTGCGATAGTCTACAGTGT
* * *
1154212 CGTTGCGAT--TTTCCA-TTT
1 CGTTGCGATAGTCTACAGTGT
1154230 CGCGTTGCGATAGTCTACAGTGT
1 --CGTTGCGATAGTCTACAGTGT
1154253 CGTTGCGATAGTCTACAGT
1 CGTTGCGATAGTCTACAGT
1154272 AAATTAAAAA
Statistics
Matches: 109, Mismatches: 18, Indels: 30
0.69 0.11 0.19
Matches are distributed among these distances:
18 6 0.06
19 12 0.11
20 27 0.25
21 46 0.42
22 12 0.11
23 6 0.06
ACGTcount: A:0.16, C:0.21, G:0.26, T:0.37
Consensus pattern (21 bp):
CGTTGCGATAGTCTACAGTGT
Found at i:1154362 original size:6 final size:6
Alignment explanation
Indices: 1154351--1154389 Score: 78
Period size: 6 Copynumber: 6.5 Consensus size: 6
1154341 GACACGTATT
1154351 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
1154390 CGAGACGAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.33, C:0.51, G:0.15, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:1154904 original size:6 final size:6
Alignment explanation
Indices: 1154888--1154932 Score: 83
Period size: 6 Copynumber: 7.7 Consensus size: 6
1154878 TCTCGTCTCG
1154888 GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTC
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTC
1154933 ATACGTGTCT
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
5 5 0.13
6 34 0.87
ACGTcount: A:0.00, C:0.18, G:0.51, T:0.31
Consensus pattern (6 bp):
GGTCGT
Found at i:1161261 original size:32 final size:32
Alignment explanation
Indices: 1161225--1161294 Score: 113
Period size: 32 Copynumber: 2.2 Consensus size: 32
1161215 GTTTTTGGTT
* *
1161225 AGATGAAAGGAGTTTGTTGTGTAAGAGATTGA
1 AGATGAAAGGAGTGTGTTATGTAAGAGATTGA
*
1161257 AGATGAAATGAGTGTGTTATGTAAGAGATTGA
1 AGATGAAAGGAGTGTGTTATGTAAGAGATTGA
1161289 AGATGA
1 AGATGA
1161295 TGTGCACAAC
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.37, C:0.00, G:0.33, T:0.30
Consensus pattern (32 bp):
AGATGAAAGGAGTGTGTTATGTAAGAGATTGA
Found at i:1161469 original size:90 final size:87
Alignment explanation
Indices: 1161361--1161538 Score: 232
Period size: 90 Copynumber: 2.0 Consensus size: 87
1161351 GTGATGAGTT
1161361 CCATTGAAATTTAAAAAAAAAATCAACCATTGAACAACGGTCAATCCAACGGTTAA-AAAGTCAA
1 CCATTGAAATTTAAAAAAAAAATCAACCATTGAACAACGGTCAATCCAAC----AATAAAGTCAA
*
1161425 AATTATACCTGTTGGAACTCGTCACG
62 AATTATACCCGTTGGAACTCGTCACG
** * ** * *
1161451 CCATTGAAATTTTTAAAAAATATTGATCGTTGAACAACGGTCAATCCAACAATAAAGTCAAAATT
1 CCATTGAAATTTAAAAAAAAAATCAACCATTGAACAACGGTCAATCCAACAATAAAGTCAAAATT
*
1161516 ATTCCCGTTGGAACTCGTCACG
66 ATACCCGTTGGAACTCGTCACG
1161538 C
1 C
1161539 TGTTGCAACT
Statistics
Matches: 78, Mismatches: 9, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
86 2 0.03
87 33 0.42
90 43 0.55
ACGTcount: A:0.40, C:0.20, G:0.13, T:0.26
Consensus pattern (87 bp):
CCATTGAAATTTAAAAAAAAAATCAACCATTGAACAACGGTCAATCCAACAATAAAGTCAAAATT
ATACCCGTTGGAACTCGTCACG
Found at i:1163469 original size:32 final size:32
Alignment explanation
Indices: 1163428--1163563 Score: 197
Period size: 32 Copynumber: 4.3 Consensus size: 32
1163418 GAGTCGAGGG
1163428 TTACCTATGTCTTTCGGGACATATGGACATGA
1 TTACCTATGTCTTTCGGGACATATGGACATGA
* *
1163460 TTACCTATGTCTTTCGGGACATATGGATAGGA
1 TTACCTATGTCTTTCGGGACATATGGACATGA
* *
1163492 TTACCTATGTCCTTCGGGACATATGGACAAGA
1 TTACCTATGTCTTTCGGGACATATGGACATGA
*
1163524 TTACCTATGT-TCTTCAGGACATATGGACAT--
1 TTACCTATGTCT-TTCGGGACATATGGACATGA
1163554 TTACCTATGT
1 TTACCTATGT
1163564 TCTTATGAAC
Statistics
Matches: 95, Mismatches: 8, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
30 10 0.11
32 85 0.89
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.35
Consensus pattern (32 bp):
TTACCTATGTCTTTCGGGACATATGGACATGA
Found at i:1164267 original size:21 final size:22
Alignment explanation
Indices: 1164237--1164285 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
1164227 AAATTTACTA
*
1164237 TAGCAAGGGTATCGGTA-CACTG
1 TAGC-AGGGTATCGATACCACTG
*
1164259 TAGCAGGGTATCGATACCCCTG
1 TAGCAGGGTATCGATACCACTG
1164281 TAGCA
1 TAGCA
1164286 TTTTGAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 11 0.46
22 13 0.54
ACGTcount: A:0.27, C:0.22, G:0.29, T:0.22
Consensus pattern (22 bp):
TAGCAGGGTATCGATACCACTG
Found at i:1164352 original size:22 final size:23
Alignment explanation
Indices: 1164309--1164353 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
1164299 TAACATTCGG
*
1164309 TACTGTTCACGGTACTGTTCATAT
1 TACTGTTCAC-GTAATGTTCATAT
1164333 TACTGTTCA-GTAATGTTCATA
1 TACTGTTCACGTAATGTTCATA
1164354 CAATATAGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 11 0.55
24 9 0.45
ACGTcount: A:0.24, C:0.18, G:0.16, T:0.42
Consensus pattern (23 bp):
TACTGTTCACGTAATGTTCATAT
Found at i:1165130 original size:28 final size:27
Alignment explanation
Indices: 1165099--1165180 Score: 83
Period size: 27 Copynumber: 3.0 Consensus size: 27
1165089 CCTTATCATC
*
1165099 TCCCCAACCTTCTCTCTCTCGTCCCCCT
1 TCCCCAACCTT-TCCCTCTCGTCCCCCT
* *
1165127 TCCCTATCCTTTCCCTCTCGTCCCCCT
1 TCCCCAACCTTTCCCTCTCGTCCCCCT
* * * *
1165154 TCCCTATCATTTCCCTCTTGTCTCCCC
1 TCCCCAACCTTTCCCTCTCGTC-CCCC
1165181 AGCCCGATGC
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
27 35 0.73
28 13 0.27
ACGTcount: A:0.06, C:0.54, G:0.04, T:0.37
Consensus pattern (27 bp):
TCCCCAACCTTTCCCTCTCGTCCCCCT
Found at i:1165148 original size:27 final size:27
Alignment explanation
Indices: 1165114--1165180 Score: 107
Period size: 27 Copynumber: 2.4 Consensus size: 27
1165104 AACCTTCTCT
*
1165114 CTCTCGTCCCCCTTCCCTATCCTTTCC
1 CTCTCGTCCCCCTTCCCTATCATTTCC
1165141 CTCTCGTCCCCCTTCCCTATCATTTCC
1 CTCTCGTCCCCCTTCCCTATCATTTCC
*
1165168 CTCTTGTCTCCCC
1 CTCTCGTC-CCCC
1165181 AGCCCGATGC
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
27 33 0.89
28 4 0.11
ACGTcount: A:0.04, C:0.54, G:0.04, T:0.37
Consensus pattern (27 bp):
CTCTCGTCCCCCTTCCCTATCATTTCC
Found at i:1166873 original size:60 final size:60
Alignment explanation
Indices: 1166779--1166954 Score: 180
Period size: 60 Copynumber: 2.9 Consensus size: 60
1166769 GGGGGACATT
** * * * *
1166779 ATTGGAATGTTTGAAAGTTTGGTGACTAATTTAGAATAAGGGTCATGGTTTGA-GGATTAA
1 ATTGGAATGTTCAAAAGTTAGG-GACTAATTTAGAATAAGAGTCATAGTTTGAGGGATGAA
* **
1166839 ATTGGAATGTTCAAAAGCTTAGGGACCAATTTAGAATGTGAGTCATAGTTT-AGGGATGAA
1 ATTGGAATGTTCAAAAG-TTAGGGACTAATTTAGAATAAGAGTCATAGTTTGAGGGATGAA
** *
1166899 ATTTAAATGTTCAAAAGTATAGGGACTGATTT-GAAATAAGAGTCATAGTTTG-GGGA
1 ATTGGAATGTTCAAAAGT-TAGGGACTAATTTAG-AATAAGAGTCATAGTTTGAGGGA
1166955 CTCATCTTGT
Statistics
Matches: 96, Mismatches: 15, Indels: 10
0.79 0.12 0.08
Matches are distributed among these distances:
59 3 0.03
60 89 0.93
61 4 0.04
ACGTcount: A:0.35, C:0.06, G:0.27, T:0.33
Consensus pattern (60 bp):
ATTGGAATGTTCAAAAGTTAGGGACTAATTTAGAATAAGAGTCATAGTTTGAGGGATGAA
Found at i:1168034 original size:23 final size:24
Alignment explanation
Indices: 1168002--1168087 Score: 88
Period size: 24 Copynumber: 3.6 Consensus size: 24
1167992 AACATTAAAC
*
1168002 AAATGCTAAACGAACATGTTCGT-A
1 AAAT-CTAAACGAACACGTTCGTGA
1168026 AAATCTAAACGAACACG-TCTGTGA
1 AAATCTAAACGAACACGTTC-GTGA
* * *
1168050 ACATATAAACGAACACATTCGTGA
1 AAATCTAAACGAACACGTTCGTGA
*
1168074 ACAT-TAAACGAACA
1 AAATCTAAACGAACA
1168088 TGTTTACGAA
Statistics
Matches: 55, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
22 2 0.04
23 24 0.44
24 27 0.49
25 2 0.04
ACGTcount: A:0.45, C:0.20, G:0.14, T:0.21
Consensus pattern (24 bp):
AAATCTAAACGAACACGTTCGTGA
Found at i:1168099 original size:47 final size:46
Alignment explanation
Indices: 1168008--1168104 Score: 106
Period size: 47 Copynumber: 2.1 Consensus size: 46
1167998 AAACAAATGC
** **
1168008 TAAACGAACATGTTCGTAAAATCTAAACGAACACGTCTGTGAACATA
1 TAAACGAACACATTCGTAAAATCTAAACGAACACGTCTACGAACA-A
* * *
1168055 TAAACGAACACATTCGTGAACAT-TAAACGAACATGTTTACGAACAA
1 TAAACGAACACATTCGT-AAAATCTAAACGAACACGTCTACGAACAA
1168101 TAAA
1 TAAA
1168105 TAAACAAACA
Statistics
Matches: 42, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
46 5 0.12
47 33 0.79
48 4 0.10
ACGTcount: A:0.45, C:0.19, G:0.13, T:0.23
Consensus pattern (46 bp):
TAAACGAACACATTCGTAAAATCTAAACGAACACGTCTACGAACAA
Found at i:1169085 original size:19 final size:19
Alignment explanation
Indices: 1169061--1169113 Score: 97
Period size: 19 Copynumber: 2.8 Consensus size: 19
1169051 GCATGGCAGT
*
1169061 CCGTGACACTGCCCTCTGC
1 CCGTGACACTGCCCTCCGC
1169080 CCGTGACACTGCCCTCCGC
1 CCGTGACACTGCCCTCCGC
1169099 CCGTGACACTGCCCT
1 CCGTGACACTGCCCT
1169114 GCATGGCAGT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.11, C:0.49, G:0.21, T:0.19
Consensus pattern (19 bp):
CCGTGACACTGCCCTCCGC
Found at i:1169281 original size:18 final size:18
Alignment explanation
Indices: 1169258--1169302 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 18
1169248 GGAGGCACCG
1169258 GGAGAAGAAAGAAA-AATA
1 GGAGAAGAAAGAAATAA-A
*
1169276 GGAGAAGGAAGAAATAAA
1 GGAGAAGAAAGAAATAAA
1169294 GGAAGAAGA
1 GG-AGAAGA
1169303 CGAAGAATCA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 16 0.70
19 7 0.30
ACGTcount: A:0.62, C:0.00, G:0.33, T:0.04
Consensus pattern (18 bp):
GGAGAAGAAAGAAATAAA
Found at i:1171026 original size:22 final size:22
Alignment explanation
Indices: 1171000--1171041 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
1170990 ATATGAGGTT
1171000 TGTCCCGAAAGACCTATGAATA
1 TGTCCCGAAAGACCTATGAATA
*
1171022 TGTCCCGAATGACCTATGAA
1 TGTCCCGAAAGACCTATGAA
1171042 ACCCTCGACT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.33, C:0.24, G:0.19, T:0.24
Consensus pattern (22 bp):
TGTCCCGAAAGACCTATGAATA
Found at i:1171676 original size:19 final size:19
Alignment explanation
Indices: 1171652--1171702 Score: 84
Period size: 19 Copynumber: 2.7 Consensus size: 19
1171642 TTTTGAGGGG
*
1171652 GTATCGATACACTGACTGT
1 GTATCGATACACTGACCGT
*
1171671 GTATCGATACACTGCCCGT
1 GTATCGATACACTGACCGT
1171690 GTATCGATACACT
1 GTATCGATACACT
1171703 TATTTCATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.25, C:0.25, G:0.20, T:0.29
Consensus pattern (19 bp):
GTATCGATACACTGACCGT
Found at i:1175242 original size:2 final size:2
Alignment explanation
Indices: 1175231--1175260 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1175221 TATCCTGTTT
1175231 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1175261 TGTGTTAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1177180 original size:19 final size:21
Alignment explanation
Indices: 1177142--1177180 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
1177132 ATTAAAATTT
*
1177142 ATATTATACAATATAAAAATA
1 ATATTATACAATAAAAAAATA
1177163 ATATTA-AC-ATAAAAAAAT
1 ATATTATACAATAAAAAAAT
1177181 CGTAAAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
20 2 0.12
21 6 0.35
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.31
Consensus pattern (21 bp):
ATATTATACAATAAAAAAATA
Found at i:1189605 original size:2 final size:2
Alignment explanation
Indices: 1189598--1189624 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1189588 TATAGTAATC
1189598 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1189625 AATTATACTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1193788 original size:27 final size:27
Alignment explanation
Indices: 1193727--1193782 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
1193717 TGTTGTGTGT
1193727 ATGCGTGTATAATACAACTCTGATATG
1 ATGCGTGTATAATACAACTCTGATATG
1193754 ATGCGTGTATAATACAACTCTGATATG
1 ATGCGTGTATAATACAACTCTGATATG
1193781 AT
1 AT
1193783 AGGTGTTTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.34, C:0.14, G:0.18, T:0.34
Consensus pattern (27 bp):
ATGCGTGTATAATACAACTCTGATATG
Found at i:1200535 original size:49 final size:49
Alignment explanation
Indices: 1200478--1200573 Score: 183
Period size: 49 Copynumber: 2.0 Consensus size: 49
1200468 AATTTCTGGG
*
1200478 AAAGATATATCATAATAGAATTTTGGTGTAAATGGTAATCTCACTTGGT
1 AAAGATATATCATAACAGAATTTTGGTGTAAATGGTAATCTCACTTGGT
1200527 AAAGATATATCATAACAGAATTTTGGTGTAAATGGTAATCTCACTTG
1 AAAGATATATCATAACAGAATTTTGGTGTAAATGGTAATCTCACTTG
1200574 CATCATCTGT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 46 1.00
ACGTcount: A:0.38, C:0.09, G:0.18, T:0.35
Consensus pattern (49 bp):
AAAGATATATCATAACAGAATTTTGGTGTAAATGGTAATCTCACTTGGT
Found at i:1201068 original size:122 final size:122
Alignment explanation
Indices: 1200850--1201070 Score: 325
Period size: 122 Copynumber: 1.8 Consensus size: 122
1200840 TGCTGTAGGA
* * * * * *
1200850 AATGCCTTCTGGTTCTTAAAGTTGTTATGTTAATCAGACATTGGGTCCTAGTAAGTTAAAGTCAG
1 AATGCCTTCTAGTTCTTAAAGTTGTTATGATAATCAAACATTGGGTCCTAGCAAGTAAAAGTCAC
* * * *
1200915 ATTCGTTGAGTCCATATCATGTTGGAGAATTTCTACAGCTTGATATGGTTTTATGAG
66 ATTCATTGAGTCCAAATCATGGTGGAAAATTTCTACAGCTTGATATGGTTTTATGAG
* *
1200972 AATGCCTTCTAGTTCTTAAAGTTGTTATGATAGTCAAACATTGTGTCCTAGCAAGTAAAAGTCAC
1 AATGCCTTCTAGTTCTTAAAGTTGTTATGATAATCAAACATTGGGTCCTAGCAAGTAAAAGTCAC
*
1201037 ATTCATTGATTCCAAATCATGGTGGAAAATTTCT
66 ATTCATTGAGTCCAAATCATGGTGGAAAATTTCT
1201071 GTGTCAGGAT
Statistics
Matches: 86, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
122 86 1.00
ACGTcount: A:0.29, C:0.14, G:0.19, T:0.37
Consensus pattern (122 bp):
AATGCCTTCTAGTTCTTAAAGTTGTTATGATAATCAAACATTGGGTCCTAGCAAGTAAAAGTCAC
ATTCATTGAGTCCAAATCATGGTGGAAAATTTCTACAGCTTGATATGGTTTTATGAG
Found at i:1201242 original size:16 final size:16
Alignment explanation
Indices: 1201221--1201251 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
1201211 GAGCAAAGGG
1201221 AAGAATGAAGGAGAAA
1 AAGAATGAAGGAGAAA
1201237 AAGAATGAAGGAGAA
1 AAGAATGAAGGAGAA
1201252 GCCCAAGACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.61, C:0.00, G:0.32, T:0.06
Consensus pattern (16 bp):
AAGAATGAAGGAGAAA
Found at i:1209866 original size:155 final size:155
Alignment explanation
Indices: 1209584--1209893 Score: 575
Period size: 155 Copynumber: 2.0 Consensus size: 155
1209574 AATGTTGTGC
1209584 GCATTTCTTTTATTATAGTCAGTCATCTCAAATTAATATTCCCATCTAATTCCCTTTTCCTTCTC
1 GCATTTCTTTTATTATAGTCAGTCATCTCAAATTAATATTCCCATCTAATTCCCTTTTCCTTCTC
***
1209649 ACAATATTCGGAGGACATTACCAATTTATTTTTTTTAAAAAATCTTCTTAAGTTGTTAAAAAGCG
66 ACAATATTCGGAGGACATTACCAATTTATTTTTAAAAAAAAATCTTCTTAAGTTGTTAAAAAGCG
1209714 ATTTTAGGGTTTAAAAATAGAAAAT
131 ATTTTAGGGTTTAAAAATAGAAAAT
*
1209739 GCATTTCTTTTATTATAGTCGGTCATCTCAAATTAATATTCCCATCTAATTCCCTTTTCCTTCTC
1 GCATTTCTTTTATTATAGTCAGTCATCTCAAATTAATATTCCCATCTAATTCCCTTTTCCTTCTC
*
1209804 ACAATATTCGGAGGACATTACCAATTTATTTTTAAAAAAAAATCTTCTTAAGTTGTTAAAAAGTG
66 ACAATATTCGGAGGACATTACCAATTTATTTTTAAAAAAAAATCTTCTTAAGTTGTTAAAAAGCG
1209869 ATTTTAGGGTTTAAAAATAGAAAAT
131 ATTTTAGGGTTTAAAAATAGAAAAT
1209894 TTCTATTAAT
Statistics
Matches: 150, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
155 150 1.00
ACGTcount: A:0.34, C:0.16, G:0.10, T:0.41
Consensus pattern (155 bp):
GCATTTCTTTTATTATAGTCAGTCATCTCAAATTAATATTCCCATCTAATTCCCTTTTCCTTCTC
ACAATATTCGGAGGACATTACCAATTTATTTTTAAAAAAAAATCTTCTTAAGTTGTTAAAAAGCG
ATTTTAGGGTTTAAAAATAGAAAAT
Found at i:1210447 original size:12 final size:12
Alignment explanation
Indices: 1210430--1210461 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
1210420 AAAGATGATT
*
1210430 GAAGAAGATGAA
1 GAAGAAGAGGAA
1210442 GAAGAAGAGGAA
1 GAAGAAGAGGAA
1210454 GAAGAAGA
1 GAAGAAGA
1210462 CAGTGACCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.59, C:0.00, G:0.38, T:0.03
Consensus pattern (12 bp):
GAAGAAGAGGAA
Found at i:1215634 original size:19 final size:20
Alignment explanation
Indices: 1215606--1215675 Score: 63
Period size: 20 Copynumber: 3.5 Consensus size: 20
1215596 ATAACTAAAA
* * *
1215606 AAATTTGCAACGCGATCT-C
1 AAATTCGCAACACGAACTCC
1215625 AAATTCGCAACACGAACTCC
1 AAATTCGCAACACGAACTCC
* **
1215645 AATTTCGCAACAC-AGTTTCC
1 AAATTCGCAACACGA-ACTCC
1215665 AAATTCGCAAC
1 AAATTCGCAAC
1215676 TCAGTTTTGA
Statistics
Matches: 42, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
19 16 0.38
20 26 0.62
ACGTcount: A:0.36, C:0.30, G:0.11, T:0.23
Consensus pattern (20 bp):
AAATTCGCAACACGAACTCC
Found at i:1215665 original size:20 final size:20
Alignment explanation
Indices: 1215624--1215695 Score: 74
Period size: 20 Copynumber: 3.6 Consensus size: 20
1215614 AACGCGATCT
**
1215624 CAAATTCGCAACAC-GAACTC
1 CAAATTCGCAACACAG-TTTC
*
1215644 CAATTTCGCAACACAGTTTC
1 CAAATTCGCAACACAGTTTC
* *
1215664 CAAATTCGCAACTCAGTTTT
1 CAAATTCGCAACACAGTTTC
*
1215684 GAAATTCGCAAC
1 CAAATTCGCAAC
1215696 TCGAATTTCT
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
20 43 0.98
21 1 0.02
ACGTcount: A:0.35, C:0.29, G:0.11, T:0.25
Consensus pattern (20 bp):
CAAATTCGCAACACAGTTTC
Found at i:1215696 original size:20 final size:20
Alignment explanation
Indices: 1215642--1215697 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
1215632 CAACACGAAC
* *
1215642 TCCAATTTCGCAACACAGTT
1 TCCAAATTCGCAACTCAGTT
1215662 TCCAAATTCGCAACTCAGTT
1 TCCAAATTCGCAACTCAGTT
**
1215682 TTGAAATTCGCAACTC
1 TCCAAATTCGCAACTC
1215698 GAATTTCTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.30, C:0.29, G:0.11, T:0.30
Consensus pattern (20 bp):
TCCAAATTCGCAACTCAGTT
Found at i:1215928 original size:22 final size:22
Alignment explanation
Indices: 1215903--1215951 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
1215893 TCACTCTCTA
* *
1215903 CGGCGACATCCGTCCCCATCTC
1 CGGCGACATCCGTCCCAATATC
*
1215925 CGGCGACATTCGTCCCAATATC
1 CGGCGACATCCGTCCCAATATC
1215947 CGGCG
1 CGGCG
1215952 CCCCCCTCCA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.16, C:0.43, G:0.22, T:0.18
Consensus pattern (22 bp):
CGGCGACATCCGTCCCAATATC
Found at i:1216402 original size:34 final size:34
Alignment explanation
Indices: 1216364--1216429 Score: 87
Period size: 34 Copynumber: 1.9 Consensus size: 34
1216354 GCGATTTTAG
* *
1216364 TTTTCGCGTTGCGAATTGCGTGTTGCGAATTTCA
1 TTTTCGAGTTGCGAATTGCATGTTGCGAATTTCA
** *
1216398 TTTTCGAGTTGCGGTTTTCATGTTGCGAATTT
1 TTTTCGAGTTGCGAATTGCATGTTGCGAATTT
1216430 AAGTTTCAAG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
34 27 1.00
ACGTcount: A:0.14, C:0.15, G:0.26, T:0.45
Consensus pattern (34 bp):
TTTTCGAGTTGCGAATTGCATGTTGCGAATTTCA
Found at i:1217982 original size:42 final size:42
Alignment explanation
Indices: 1217928--1218075 Score: 215
Period size: 42 Copynumber: 3.5 Consensus size: 42
1217918 ATCCCCCACT
* * ** * *
1217928 TCGACACCGAGATCCATCACCTCATCGAGCCTCTTCTCCACT
1 TCGACACCGAGAGCCATCACCTGATCGAGCCGATTCTACACC
* *
1217970 TCGACACTGAGATCCATCACCTGATCGAGCCGATTCTACACC
1 TCGACACCGAGAGCCATCACCTGATCGAGCCGATTCTACACC
*
1218012 TCGACACCGAGAGCCATCACCTGATCGAGCCGATTATACACC
1 TCGACACCGAGAGCCATCACCTGATCGAGCCGATTCTACACC
1218054 TCGACACCGAGAGCCATCACCT
1 TCGACACCGAGAGCCATCACCT
1218076 ATTCCATCAT
Statistics
Matches: 97, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 97 1.00
ACGTcount: A:0.26, C:0.39, G:0.16, T:0.20
Consensus pattern (42 bp):
TCGACACCGAGAGCCATCACCTGATCGAGCCGATTCTACACC
Found at i:1218011 original size:21 final size:21
Alignment explanation
Indices: 1217987--1218054 Score: 52
Period size: 21 Copynumber: 3.2 Consensus size: 21
1217977 TGAGATCCAT
1217987 CACCTGATCGAGCCGATTCTA
1 CACCTGATCGAGCCGATTCTA
** *
1218008 CACCTCGA-C-A-CCGAGAGCCA
1 CACCT-GATCGAGCCGA-TTCTA
*
1218028 TCACCTGATCGAGCCGATTATA
1 -CACCTGATCGAGCCGATTCTA
1218050 CACCT
1 CACCT
1218055 CGACACCGAG
Statistics
Matches: 34, Mismatches: 7, Indels: 12
0.64 0.13 0.23
Matches are distributed among these distances:
19 4 0.12
20 5 0.15
21 17 0.50
22 4 0.12
23 4 0.12
ACGTcount: A:0.26, C:0.37, G:0.18, T:0.19
Consensus pattern (21 bp):
CACCTGATCGAGCCGATTCTA
Found at i:1218201 original size:21 final size:21
Alignment explanation
Indices: 1218175--1218239 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
1218165 ACCTCCAAGG
1218175 GATGAGTTAGGTGCTTTACGT
1 GATGAGTTAGGTGCTTTACGT
* *
1218196 GATGAGGTCA-ATGCTTTACGT
1 GATGA-GTTAGGTGCTTTACGT
* * *
1218217 GATGAGGTCGGTGCTTAACGT
1 GATGAGTTAGGTGCTTTACGT
1218238 GA
1 GA
1218240 CGACAATGGT
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
20 1 0.03
21 31 0.89
22 3 0.09
ACGTcount: A:0.22, C:0.12, G:0.34, T:0.32
Consensus pattern (21 bp):
GATGAGTTAGGTGCTTTACGT
Found at i:1218302 original size:42 final size:43
Alignment explanation
Indices: 1218256--1218349 Score: 115
Period size: 42 Copynumber: 2.2 Consensus size: 43
1218246 TGGTGCATGG
*
1218256 CGTGATGAGGCAA-GGAT-TTTACGTGGTAAGGTAGCTGTTTTA
1 CGTGATGAGGCAATGG-TCTTTACGTGGTAAGGTAGCTGCTTTA
* *
1218298 CGTGATGA--CAATGGTGCTTTACGTGGTGAGGTATCTGCTTTA
1 CGTGATGAGGCAATGGT-CTTTACGTGGTAAGGTAGCTGCTTTA
1218340 CGTGATGAGG
1 CGTGATGAGG
1218350 TAGCTGCTCT
Statistics
Matches: 44, Mismatches: 3, Indels: 8
0.80 0.05 0.15
Matches are distributed among these distances:
40 4 0.09
41 2 0.05
42 38 0.86
ACGTcount: A:0.21, C:0.12, G:0.34, T:0.33
Consensus pattern (43 bp):
CGTGATGAGGCAATGGTCTTTACGTGGTAAGGTAGCTGCTTTA
Found at i:1218328 original size:63 final size:63
Alignment explanation
Indices: 1218184--1218365 Score: 172
Period size: 63 Copynumber: 2.9 Consensus size: 63
1218174 GGATGAGTTA
* * * *
1218184 GGTGCTTTACGTGATGAGGTCAATGCTTTACGTGATGAGGTCGGTGCTTAACGTGACGACAAT
1 GGTGCTTTACGTGATGAGGTCAAGGCTTTACGTGATAAGGTAGCTGCTTAACGTGACGACAAT
* ** * * * * *
1218247 GGTGCATGGCGTGATGAGG-CAAGGATTTTACGTGGTAAGGTAGCTGTTTTACGTGATGACAAT
1 GGTGCTTTACGTGATGAGGTCAAGG-CTTTACGTGATAAGGTAGCTGCTTAACGTGACGACAAT
* ** *
1218310 GGTGCTTTACGTGGTGAGGT-ATCTGCTTTACGTGATGAGGTAGCTGCTCT-ACGTGA
1 GGTGCTTTACGTGATGAGGTCA-AGGCTTTACGTGATAAGGTAGCTGCT-TAACGTGA
1218366 GATTATTTCA
Statistics
Matches: 93, Mismatches: 22, Indels: 8
0.76 0.18 0.07
Matches are distributed among these distances:
62 4 0.04
63 87 0.94
64 2 0.02
ACGTcount: A:0.21, C:0.14, G:0.34, T:0.31
Consensus pattern (63 bp):
GGTGCTTTACGTGATGAGGTCAAGGCTTTACGTGATAAGGTAGCTGCTTAACGTGACGACAAT
Found at i:1218336 original size:21 final size:21
Alignment explanation
Indices: 1218273--1218365 Score: 89
Period size: 21 Copynumber: 4.4 Consensus size: 21
1218263 AGGCAAGGAT
* * *
1218273 TTTACGTGGTAAGGTAGCTGT
1 TTTACGTGATGAGGTAGCTGC
** *
1218294 TTTACGTGATGA-CAATGGTGC
1 TTTACGTGATGAGGTA-GCTGC
* *
1218315 TTTACGTGGTGAGGTATCTGC
1 TTTACGTGATGAGGTAGCTGC
1218336 TTTACGTGATGAGGTAGCTGC
1 TTTACGTGATGAGGTAGCTGC
*
1218357 TCTACGTGA
1 TTTACGTGA
1218366 GATTATTTCA
Statistics
Matches: 56, Mismatches: 14, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
20 1 0.02
21 54 0.96
22 1 0.02
ACGTcount: A:0.19, C:0.14, G:0.31, T:0.35
Consensus pattern (21 bp):
TTTACGTGATGAGGTAGCTGC
Found at i:1218363 original size:42 final size:42
Alignment explanation
Indices: 1218275--1218364 Score: 101
Period size: 42 Copynumber: 2.1 Consensus size: 42
1218265 GCAAGGATTT
* * *
1218275 TACGTGGTAAGGTAGCTGTTTTACGTGATGACAATGGTGCTT
1 TACGTGGTAAGGTAGCTGCTTTACGTGATGACAATGCTGCTC
* * **
1218317 TACGTGGTGAGGTATCTGCTTTACGTGATGA-GGTAGCTGCTC
1 TACGTGGTAAGGTAGCTGCTTTACGTGATGACAAT-GCTGCTC
1218359 TACGTG
1 TACGTG
1218365 AGATTATTTC
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
41 1 0.03
42 39 0.98
ACGTcount: A:0.19, C:0.14, G:0.32, T:0.34
Consensus pattern (42 bp):
TACGTGGTAAGGTAGCTGCTTTACGTGATGACAATGCTGCTC
Found at i:1218677 original size:21 final size:21
Alignment explanation
Indices: 1218651--1218713 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
1218641 AGAAGCTCGT
1218651 TCCACCTATCATTGTTCAAGA
1 TCCACCTATCATTGTTCAAGA
*
1218672 TCCACCTCTCATTGTTCAAGA
1 TCCACCTATCATTGTTCAAGA
** *
1218693 TTTACCTATCATCGTTCAAGA
1 TCCACCTATCATTGTTCAAGA
1218714 GGCCCCTCCC
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.27, C:0.29, G:0.10, T:0.35
Consensus pattern (21 bp):
TCCACCTATCATTGTTCAAGA
Found at i:1218726 original size:21 final size:21
Alignment explanation
Indices: 1218664--1218760 Score: 70
Period size: 21 Copynumber: 4.6 Consensus size: 21
1218654 ACCTATCATT
* * *
1218664 GTTCAAGATCCACCTCTCATT
1 GTTCAAGAGCCACCTCCCATC
*** **
1218685 GTTCAAGATTTACCTATCATC
1 GTTCAAGAGCCACCTCCCATC
1218706 GTTCAAGAGGCC-CCTCCCATC
1 GTTCAAGA-GCCACCTCCCATC
* * *
1218727 ATTCAGGATCCACCTCCCATC
1 GTTCAAGAGCCACCTCCCATC
*
1218748 GTTCAAGATCCAC
1 GTTCAAGAGCCAC
1218761 ATGGCATACT
Statistics
Matches: 60, Mismatches: 14, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
20 2 0.03
21 58 0.97
ACGTcount: A:0.25, C:0.35, G:0.12, T:0.28
Consensus pattern (21 bp):
GTTCAAGAGCCACCTCCCATC
Found at i:1222924 original size:24 final size:24
Alignment explanation
Indices: 1222890--1222943 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
1222880 CTGAAACATC
1222890 ATCAAAATCTGAGTATTGACCAAG
1 ATCAAAATCTGAGTATTGACCAAG
* *
1222914 ATCAAAGTCTGGGTATTGACCAAG
1 ATCAAAATCTGAGTATTGACCAAG
1222938 ATCAAA
1 ATCAAA
1222944 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.17, G:0.19, T:0.24
Consensus pattern (24 bp):
ATCAAAATCTGAGTATTGACCAAG
Found at i:1223092 original size:12 final size:12
Alignment explanation
Indices: 1223071--1223104 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1223061 GGTTGTGAGT
*
1223071 TTTGAGATTGTG
1 TTTGATATTGTG
1223083 TTTGATATTGTG
1 TTTGATATTGTG
*
1223095 TTTGGTATTG
1 TTTGATATTG
1223105 GAAATGTGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.29, T:0.56
Consensus pattern (12 bp):
TTTGATATTGTG
Found at i:1223946 original size:40 final size:41
Alignment explanation
Indices: 1223902--1224058 Score: 148
Period size: 40 Copynumber: 3.9 Consensus size: 41
1223892 TTGCAAAATT
* *
1223902 AAAATTCGTGTTACGAATTCGAAAATCGAGTTGCGAAAA-C
1 AAAATTCGTGTTGCGAATTAGAAAATCGAGTTGCGAAAAGC
*
1223942 AAAATTCGTGTTGCGAATTAGAAAATC-ATGTTGCGAAAAGG
1 AAAATTCGTGTTGCGAATTAGAAAATCGA-GTTGCGAAAAGC
* *
1223983 AAACTT-GTGTTGCGAATTTA-AAAATCGCGTTGCGAAAA--
1 AAAATTCGTGTTGCGAA-TTAGAAAATCGAGTTGCGAAAAGC
* * * *
1224021 AGAAATTTGAGTTGTGAATTCAG-AAATCTAGTTGCGAA
1 A-AAATTCGTGTTGCGAATT-AGAAAATCGAGTTGCGAA
1224059 TTTGAAATTC
Statistics
Matches: 99, Mismatches: 10, Indels: 16
0.79 0.08 0.13
Matches are distributed among these distances:
38 1 0.01
39 7 0.07
40 83 0.84
41 8 0.08
ACGTcount: A:0.38, C:0.11, G:0.22, T:0.28
Consensus pattern (41 bp):
AAAATTCGTGTTGCGAATTAGAAAATCGAGTTGCGAAAAGC
Found at i:1223954 original size:20 final size:20
Alignment explanation
Indices: 1223902--1223998 Score: 65
Period size: 20 Copynumber: 4.8 Consensus size: 20
1223892 TTGCAAAATT
* **
1223902 AAAATTCGTGTTACGAATTC
1 AAAATTCGTGTTGCGAAAAC
*
1223922 GAAAA-TCGAGTTGCGAAAAC
1 -AAAATTCGTGTTGCGAAAAC
* *
1223942 AAAATTCGTGTTGCGAATTAG
1 AAAATTCGTGTTGCGAA-AAC
* *
1223963 AAAA-TCATGTTGCGAAAAGG
1 AAAATTCGTGTTGCGAAAA-C
*
1223983 AAACTT-GTGTTGCGAA
1 AAAATTCGTGTTGCGAA
1223999 TTTAAAAATC
Statistics
Matches: 61, Mismatches: 11, Indels: 9
0.75 0.14 0.11
Matches are distributed among these distances:
19 5 0.08
20 46 0.75
21 10 0.16
ACGTcount: A:0.38, C:0.12, G:0.23, T:0.27
Consensus pattern (20 bp):
AAAATTCGTGTTGCGAAAAC
Found at i:1224027 original size:80 final size:80
Alignment explanation
Indices: 1223909--1224058 Score: 189
Period size: 80 Copynumber: 1.9 Consensus size: 80
1223899 ATTAAAATTC
* *
1223909 GTGTTACGAATTCGAAAATCGAGTTGCGAAAACAAAATTCGTGTTGCGAATT-AGAAAATC-ATG
1 GTGTTACGAATTCAAAAATCGAGTTGCGAAAACAAAATTCGAGTTGCGAATTCAG-AAATCTA-G
1223972 TTGCGAAAAGGAAACTT
64 TTGCGAAAAGGAAACTT
* * * * *
1223989 GTGTTGCGAATTTAAAAATCGCGTTGCGAAAA-AGAAATTTGAGTTGTGAATTCAGAAATCTAGT
1 GTGTTACGAATTCAAAAATCGAGTTGCGAAAACA-AAATTCGAGTTGCGAATTCAGAAATCTAGT
1224053 TGCGAA
65 TGCGAA
1224059 TTTGAAATTC
Statistics
Matches: 60, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
79 1 0.02
80 56 0.93
81 3 0.05
ACGTcount: A:0.37, C:0.11, G:0.23, T:0.28
Consensus pattern (80 bp):
GTGTTACGAATTCAAAAATCGAGTTGCGAAAACAAAATTCGAGTTGCGAATTCAGAAATCTAGTT
GCGAAAAGGAAACTT
Found at i:1224141 original size:101 final size:98
Alignment explanation
Indices: 1224043--1224263 Score: 241
Period size: 101 Copynumber: 2.2 Consensus size: 98
1224033 TGTGAATTCA
*
1224043 GAAATCTAGTTGCGAATTTGAAATTCCGTGTTGCGAATACCAAATT-CGCAACGCCAATTTGGGA
1 GAAATCT-GTTGCGAATTTGAAA-T-CGAGTTGCGAATACCAAATTCCGCAACGCCAATTT-GGA
1224107 AA-TGCGTTGTGAAATTGGAGTTTGTGTTGCGAATTT
62 AATTGCGTTGTGAAATTGGAGTTTGTGTTGCGAATTT
* * * *** *
1224143 GAAAATCGCGTTGCGAATTCAT-AAATCGAGTTGCGAATTCGAAATTCCGCTTTGCGAATTTGGA
1 G-AAATC-TGTTGCGAATT--TGAAATCGAGTTGCGAATACCAAATTCCGCAACGCCAATTTGGA
* *
1224207 AATTGTGTTGTGAAATTGGAGTTCGTGTTGCGAATTT
62 AATTGCGTTGTGAAATTGGAGTTTGTGTTGCGAATTT
*
1224244 GAGATCGTGTTGCGAATTTG
1 GAAATC-TGTTGCGAATTTG
1224264 TTGGTTATTT
Statistics
Matches: 102, Mismatches: 12, Indels: 15
0.79 0.09 0.12
Matches are distributed among these distances:
98 1 0.01
100 38 0.37
101 59 0.58
102 3 0.03
103 1 0.01
ACGTcount: A:0.27, C:0.13, G:0.26, T:0.34
Consensus pattern (98 bp):
GAAATCTGTTGCGAATTTGAAATCGAGTTGCGAATACCAAATTCCGCAACGCCAATTTGGAAATT
GCGTTGTGAAATTGGAGTTTGTGTTGCGAATTT
Found at i:1224157 original size:20 final size:20
Alignment explanation
Indices: 1224130--1224263 Score: 103
Period size: 20 Copynumber: 6.7 Consensus size: 20
1224120 ATTGGAGTTT
1224130 GTGTTGCGAATTTGAAAATC
1 GTGTTGCGAATTTGAAAATC
* *
1224150 GCGTTGCGAA-TTCATAAATC
1 GTGTTGCGAATTTGA-AAATC
* * *
1224170 GAGTTGCGAATTCGAAATTCC
1 GTGTTGCGAATTTGAAAAT-C
* *
1224191 GCT-TTGCGAATTTGGAAATT
1 G-TGTTGCGAATTTGAAAATC
* * * **
1224211 GTGTTGTGAAATTGGAGTTC
1 GTGTTGCGAATTTGAAAATC
*
1224231 GTGTTGCGAATTTG-AGATC
1 GTGTTGCGAATTTGAAAATC
1224250 GTGTTGCGAATTTG
1 GTGTTGCGAATTTG
1224264 TTGGTTATTT
Statistics
Matches: 90, Mismatches: 19, Indels: 11
0.75 0.16 0.09
Matches are distributed among these distances:
19 22 0.24
20 51 0.57
21 17 0.19
ACGTcount: A:0.25, C:0.12, G:0.28, T:0.36
Consensus pattern (20 bp):
GTGTTGCGAATTTGAAAATC
Found at i:1227202 original size:131 final size:129
Alignment explanation
Indices: 1227015--1227254 Score: 331
Period size: 131 Copynumber: 1.8 Consensus size: 129
1227005 AGAGACGATG
* * *
1227015 ATAACACAATTTCTAAGTGATGAGGATGACTGGTTATCTAAGGGTGACACGACTCCTACATGATG
1 ATAACACAATTCCTAAGTGATGAGGACGACTGGTTATCTAAGGGTGACAAGACTCCTACATGATG
* * * *
1227080 AGGA-GTTATGGTCGGTGGATGACATGGTTCTTACGTGATGAGGACGACATGCAATCTGTAGGGA
66 AGAAGGTT-TGGTC-G-GGATAACACGGTTCCTACGTGATGAGGACGACATGCAATCTGTAGGGA
1227144 TT
128 TT
* * * *
1227146 ATAACACGATTCCTACGTGATGAGGACGGCTGGTTATCTAAGGGTGACATAG-CTCCTACGTGAT
1 ATAACACAATTCCTAAGTGATGAGGACGACTGGTTATCTAAGGGTGACA-AGACTCCTACATGAT
1227210 GAGAAGGTTTGGTCGGGATAACACGGTTCCTACGTGATGAGGACG
65 GAGAAGGTTTGGTCGGGATAACACGGTTCCTACGTGATGAGGACG
1227255 GCTGACCATC
Statistics
Matches: 96, Mismatches: 11, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
129 27 0.28
130 1 0.01
131 64 0.67
132 4 0.04
ACGTcount: A:0.27, C:0.16, G:0.30, T:0.27
Consensus pattern (129 bp):
ATAACACAATTCCTAAGTGATGAGGACGACTGGTTATCTAAGGGTGACAAGACTCCTACATGATG
AGAAGGTTTGGTCGGGATAACACGGTTCCTACGTGATGAGGACGACATGCAATCTGTAGGGATT
Found at i:1227425 original size:64 final size:65
Alignment explanation
Indices: 1227278--1227613 Score: 351
Period size: 64 Copynumber: 5.2 Consensus size: 65
1227268 AGGGATAATG
* * * * *
1227278 GTTTTAAGAGAAATTGTCTCAAGAGAGACAGAATTCG-TTCAAGGGAAACGACTCAAAGATGA-T
1 GTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTCGTTTCAAGGAAAACGACTCAAAGATGATT
*
1227341 GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTCGTTTCAA-GAAAACGACTCAAAGATGATT
1 GTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTCGTTTCAAGGAAAACGACTCAAAGATGATT
* * * * * *
1227405 ATTTCAAGAGAATCTATCTCAAGAGAGACAAAATTAGTTTAAAGGGAAACGACTCAAAGGTG-TT
1 GTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTCGTTTCAAGGAAAACGACTCAAAGATGATT
* * * * **
1227469 GTTTCAAGACAAACTATCTCGAGAGAGACAAAATATTGTTTCAATGAAAACAGACTCAAAGATCT
1 GTTTCAAGAGAAACTATCTCAAGAGAGACAAAAT-TCGTTTCAAGGAAAAC-GACTCAAAGATGA
1227534 TT
64 TT
* * * * * *
1227536 GTTTTAAGAGAAATTGTCTCAAGAGAGACTAAATTTTGTTTCAAGGGAAATA-AACTCAAAGACT
1 GTTTCAAGAGAAACTATCTCAAGAGAGAC-AAAATTCGTTTCAA-GGAAA-ACGACTCAAAGA-T
*
1227600 -TTT
62 GATT
1227603 GTTTCAAGAGA
1 GTTTCAAGAGA
1227614 GACAAAATTT
Statistics
Matches: 233, Mismatches: 30, Indels: 16
0.84 0.11 0.06
Matches are distributed among these distances:
63 52 0.22
64 76 0.33
65 28 0.12
66 10 0.04
67 57 0.24
68 9 0.04
69 1 0.00
ACGTcount: A:0.41, C:0.13, G:0.19, T:0.26
Consensus pattern (65 bp):
GTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTCGTTTCAAGGAAAACGACTCAAAGATGATT
Found at i:1227461 original size:128 final size:131
Alignment explanation
Indices: 1227283--1227613 Score: 411
Period size: 128 Copynumber: 2.5 Consensus size: 131
1227273 TAATGGTTTT
* * * *
1227283 AAGAGAAATTGTCTCAAGAGAGACAGAATTCG-TTCAAGGGAAACGACTCAAAGATGATGTTTCA
1 AAGAGAAATTATCTCAAGAGAGACAAAATTAGTTTCAAGGGAAACGACTCAAAGATGTTGTTTCA
* *
1227347 AGAGAAACTGTCTCAAGAGAGACAAAAT-TCGTTTCAA-GAAAAC-GACTCAAAGATGATTATTT
66 AGAGAAACTATCTCAAGAGAGACAAAATATCGTTTCAATGAAAACAGACTCAAAGATCATTATTT
1227409 C
131 C
* *
1227410 AAGAG-AATCTATCTCAAGAGAGACAAAATTAGTTTAAAGGGAAACGACTCAAAGGTGTTGTTTC
1 AAGAGAAAT-TATCTCAAGAGAGACAAAATTAGTTTCAAGGGAAACGACTCAAAGATGTTGTTTC
* * * * *
1227474 AAGACAAACTATCTCGAGAGAGACAAAATATTGTTTCAATGAAAACAGACTCAAAGATCTTTGTT
65 AAGAGAAACTATCTCAAGAGAGACAAAATATCGTTTCAATGAAAACAGACTCAAAGATCATTATT
*
1227539 TT
130 TC
* * * ** *
1227541 AAGAGAAATTGTCTCAAGAGAGACTAAATTTTGTTTCAAGGGAAATAAACTCAAAGACTTTTGTT
1 AAGAGAAATTATCTCAAGAGAGAC-AAAATTAGTTTCAAGGGAAA-CGACTCAAAGA-TGTTGTT
1227606 TCAAGAGA
63 TCAAGAGA
1227614 GACAAAATTT
Statistics
Matches: 172, Mismatches: 23, Indels: 11
0.83 0.11 0.05
Matches are distributed among these distances:
126 3 0.02
127 25 0.15
128 54 0.31
129 8 0.05
130 6 0.03
131 35 0.20
132 20 0.12
133 8 0.05
134 13 0.08
ACGTcount: A:0.41, C:0.14, G:0.19, T:0.26
Consensus pattern (131 bp):
AAGAGAAATTATCTCAAGAGAGACAAAATTAGTTTCAAGGGAAACGACTCAAAGATGTTGTTTCA
AGAGAAACTATCTCAAGAGAGACAAAATATCGTTTCAATGAAAACAGACTCAAAGATCATTATTT
C
Found at i:1227656 original size:37 final size:37
Alignment explanation
Indices: 1227606--1227702 Score: 106
Period size: 38 Copynumber: 2.6 Consensus size: 37
1227596 GACTTTTGTT
* *
1227606 TCAAGAGAGACAAAATTTGTTTTGAGTA-AAAATTGTC
1 TCAAGCGAGACAAAATTTGTTTTGAG-AGAAAACTGTC
* * * *
1227643 TCAAGTGTGACAAAATTTTCTTTTTAGAGAAAACTGTC
1 TCAAGCGAGACAAAA-TTTGTTTTGAGAGAAAACTGTC
*
1227681 TCAAGCGAGAAAAAATTTGTTT
1 TCAAGCGAGACAAAATTTGTTT
1227703 CTAAAAAAAA
Statistics
Matches: 49, Mismatches: 9, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
37 20 0.41
38 29 0.59
ACGTcount: A:0.38, C:0.10, G:0.18, T:0.34
Consensus pattern (37 bp):
TCAAGCGAGACAAAATTTGTTTTGAGAGAAAACTGTC
Found at i:1233021 original size:29 final size:29
Alignment explanation
Indices: 1232988--1233054 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 29
1232978 TAAATATAAG
*
1232988 CATTCAAAGTT-AAACATTCAAACCAAAAC
1 CATTCAAA-TTCAAACATTCAAACCAAAAA
* *
1233017 CATTCAAATTCAAACGTTCAATCCAAAAA
1 CATTCAAATTCAAACATTCAAACCAAAAA
*
1233046 CATTAAAAT
1 CATTCAAAT
1233055 GTTTAACAAG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 2 0.06
29 31 0.94
ACGTcount: A:0.51, C:0.22, G:0.03, T:0.24
Consensus pattern (29 bp):
CATTCAAATTCAAACATTCAAACCAAAAA
Found at i:1235077 original size:20 final size:23
Alignment explanation
Indices: 1235054--1235107 Score: 87
Period size: 23 Copynumber: 2.5 Consensus size: 23
1235044 ACCCCGTAGA
1235054 GGGTATCGGTA-CC-CTC-AAGG
1 GGGTATCGGTACCCACTCAAAGG
1235074 GGGTATCGGTACCCACTCAAAGG
1 GGGTATCGGTACCCACTCAAAGG
1235097 GGGTATCGGTA
1 GGGTATCGGTA
1235108 GTACCCATGC
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
20 11 0.35
21 2 0.06
22 3 0.10
23 15 0.48
ACGTcount: A:0.22, C:0.22, G:0.35, T:0.20
Consensus pattern (23 bp):
GGGTATCGGTACCCACTCAAAGG
Found at i:1235127 original size:25 final size:22
Alignment explanation
Indices: 1235054--1235129 Score: 86
Period size: 20 Copynumber: 3.4 Consensus size: 22
1235044 ACCCCGTAGA
1235054 GGGTATC-GGTACCC-TCAAGG
1 GGGTATCGGGTACCCATCAAGG
1235074 GGGTATC-GGTACCCACTCAAAGG
1 GGGTATCGGGTACCCA-TC-AAGG
1235097 GGGTATCGGTAGTACCCATGCAAGG
1 GGGTATCGG--GTACCCAT-CAAGG
1235122 GGGTATCG
1 GGGTATCG
1235130 ATACCTAGCC
Statistics
Matches: 49, Mismatches: 0, Indels: 9
0.84 0.00 0.16
Matches are distributed among these distances:
20 14 0.29
22 2 0.04
23 11 0.22
24 1 0.02
25 13 0.27
26 8 0.16
ACGTcount: A:0.22, C:0.22, G:0.36, T:0.20
Consensus pattern (22 bp):
GGGTATCGGGTACCCATCAAGG
Found at i:1240958 original size:21 final size:20
Alignment explanation
Indices: 1240913--1240971 Score: 100
Period size: 20 Copynumber: 2.9 Consensus size: 20
1240903 AAATCTTACA
*
1240913 TGGGGGTATCGGTACCCTCT
1 TGGGGGTATCAGTACCCTCT
1240933 TGGGGGTATCAGTACCCTCT
1 TGGGGGTATCAGTACCCTCT
1240953 TGGGGGGTATCAGTACCCT
1 T-GGGGGTATCAGTACCCT
1240972 ATGGGCAATA
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
20 20 0.54
21 17 0.46
ACGTcount: A:0.14, C:0.24, G:0.34, T:0.29
Consensus pattern (20 bp):
TGGGGGTATCAGTACCCTCT
Found at i:1241449 original size:33 final size:31
Alignment explanation
Indices: 1241416--1241480 Score: 89
Period size: 31 Copynumber: 2.2 Consensus size: 31
1241406 GCAAAGAATG
1241416 ATGA-AAAATAACACAAACAAAAGAGAAAAA
1 ATGAGAAAATAACACAAACAAAAGAGAAAAA
** *
1241446 ATGAGTTAGTAACACAAACAAAAGAG-AAAA
1 ATGAGAAAATAACACAAACAAAAGAGAAAAA
1241476 ATGAG
1 ATGAG
1241481 TTAGTACAAG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
30 13 0.42
31 18 0.58
ACGTcount: A:0.65, C:0.09, G:0.15, T:0.11
Consensus pattern (31 bp):
ATGAGAAAATAACACAAACAAAAGAGAAAAA
Found at i:1241478 original size:30 final size:31
Alignment explanation
Indices: 1241424--1241486 Score: 119
Period size: 31 Copynumber: 2.1 Consensus size: 31
1241414 TGATGAAAAA
1241424 TAACACAAACAAAAGAGAAAAAATGAGTTAG
1 TAACACAAACAAAAGAGAAAAAATGAGTTAG
1241455 TAACACAAACAAAAGAG-AAAAATGAGTTAG
1 TAACACAAACAAAAGAGAAAAAATGAGTTAG
1241485 TA
1 TA
1241487 CAAGCAAGAT
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 15 0.47
31 17 0.53
ACGTcount: A:0.60, C:0.10, G:0.16, T:0.14
Consensus pattern (31 bp):
TAACACAAACAAAAGAGAAAAAATGAGTTAG
Found at i:1242547 original size:15 final size:16
Alignment explanation
Indices: 1242527--1242564 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
1242517 AACGTCTTTT
1242527 AAAAAT-AATTTTAAG
1 AAAAATCAATTTTAAG
*
1242542 AAAAATCATTTTTAAG
1 AAAAATCAATTTTAAG
1242558 ACAAAAT
1 A-AAAAT
1242565 TTGTTATGTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 6 0.30
16 9 0.45
17 5 0.25
ACGTcount: A:0.58, C:0.05, G:0.05, T:0.32
Consensus pattern (16 bp):
AAAAATCAATTTTAAG
Found at i:1245454 original size:18 final size:18
Alignment explanation
Indices: 1245431--1245554 Score: 158
Period size: 18 Copynumber: 6.9 Consensus size: 18
1245421 ACGTACAATT
*
1245431 TGTCCCGTAGGACCACTA
1 TGTCCCGAAGGACCACTA
** *
1245449 TGTCCCGAAAAACCACTG
1 TGTCCCGAAGGACCACTA
1245467 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
*
1245485 TGTCCCGAAGGAGCACTA
1 TGTCCCGAAGGACCACTA
* *
1245503 TGTCCCGAAAGACCATTA
1 TGTCCCGAAGGACCACTA
*
1245521 TGTCCTGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
* *
1245539 TGTCCCAAAAGACCAC
1 TGTCCCGAAGGACCAC
1245555 GTTGACCCTC
Statistics
Matches: 89, Mismatches: 17, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 89 1.00
ACGTcount: A:0.30, C:0.31, G:0.20, T:0.19
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:1245502 original size:54 final size:54
Alignment explanation
Indices: 1245431--1245554 Score: 176
Period size: 54 Copynumber: 2.3 Consensus size: 54
1245421 ACGTACAATT
* *
1245431 TGTCCCGTAGGACCACTATGTCCCGAAAAACCACTGTGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTATGTCCCGAAAAACCACTATGTCCCGAAGGACCACTA
* * * *
1245485 TGTCCCGAAGGAGCACTATGTCCCGAAAGACCATTATGTCCTGAAGGACCACTA
1 TGTCCCGAAGGACCACTATGTCCCGAAAAACCACTATGTCCCGAAGGACCACTA
* *
1245539 TGTCCCAAAAGACCAC
1 TGTCCCGAAGGACCAC
1245555 GTTGACCCTC
Statistics
Matches: 61, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
54 61 1.00
ACGTcount: A:0.30, C:0.31, G:0.20, T:0.19
Consensus pattern (54 bp):
TGTCCCGAAGGACCACTATGTCCCGAAAAACCACTATGTCCCGAAGGACCACTA
Done.