Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007761.1 Hibiscus syriacus cultivar Beakdansim tig00110030_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: 1497221
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 7
Found at i:1159909 original size:20 final size:20
Alignment explanation
Indices: 1159879--1160074 Score: 126
Period size: 20 Copynumber: 9.7 Consensus size: 20
1159869 GTTTCCAGAT
*
1159879 TCGCAACGCGATTCTGACTA
1 TCGCAATGCGATTCTGACTA
* ** *
1159899 TCGCATTGCGATT-TTCCAAA
1 TCGCAATGCGATTCTGAC-TA
** *
1159919 TCCGCGTTGCGATTTTCCGACTA
1 T-CGCAATGCGA--TTCTGACTA
* * *
1159942 TCGCAATGCGAATATGTA-AA
1 TCGCAATGCGATTCTG-ACTA
* *
1159962 TCGTAATGCGATTATGACTA
1 TCGCAATGCGATTCTGACTA
* *
1159982 TCGCAACGCAATTCTGACTA
1 TCGCAATGCGATTCTGACTA
* * *
1160002 TCGCAACGCGATTCTGATTG
1 TCGCAATGCGATTCTGACTA
* * *
1160022 TCGCAACGTGATTCTAACTA
1 TCGCAATGCGATTCTGACTA
* *
1160042 TCGCAACGCGATGCTGACTA
1 TCGCAATGCGATTCTGACTA
1160062 TCGCAATGCGATT
1 TCGCAATGCGATT
1160075 TTCAAAGCGC
Statistics
Matches: 134, Mismatches: 35, Indels: 14
0.73 0.19 0.08
Matches are distributed among these distances:
19 3 0.02
20 108 0.81
21 10 0.07
22 8 0.06
23 4 0.03
24 1 0.01
ACGTcount: A:0.26, C:0.25, G:0.20, T:0.29
Consensus pattern (20 bp):
TCGCAATGCGATTCTGACTA
Found at i:1160767 original size:20 final size:20
Alignment explanation
Indices: 1160678--1160785 Score: 103
Period size: 20 Copynumber: 5.5 Consensus size: 20
1160668 AAAATCGCAA
*
1160678 TGCGATTTT-AGTTTCGCGT
1 TGCGATTTTCATTTTCGCGT
*
1160697 TACGATTTTCA-TTTCGCGT
1 TGCGATTTTCATTTTCGCGT
** **
1160716 TGCGATAGTCAAATTCGCGT
1 TGCGATTTTCATTTTCGCGT
** *
1160736 TGCGATAGTCATTTTCGTGT
1 TGCGATTTTCATTTTCGCGT
*
1160756 TGCGATTTTCATTTTTCGTGT
1 TGCGATTTTCA-TTTTCGCGT
1160777 TGCGATTTT
1 TGCGATTTT
1160786 AAGTTTCAGA
Statistics
Matches: 76, Mismatches: 10, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
19 24 0.32
20 34 0.45
21 18 0.24
ACGTcount: A:0.15, C:0.17, G:0.22, T:0.46
Consensus pattern (20 bp):
TGCGATTTTCATTTTCGCGT
Found at i:1162805 original size:40 final size:39
Alignment explanation
Indices: 1162761--1162867 Score: 135
Period size: 40 Copynumber: 2.7 Consensus size: 39
1162751 GCGATTCTCT
1162761 CGTTGCGATAGTCAAATTCGCGTTGCAATAGTCAAATTCG
1 CGTTGCGATAGTC-AATTCGCGTTGCAATAGTCAAATTCG
* * * **
1162801 CGTTGCGATAGTCATTTTCGCGCTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCA-ATTCGCGTTGCAATAGTCAAATTCG
*
1162841 CGTTGCGATAGTC-ATTCGTGTTGCAAT
1 CGTTGCGATAGTCAATTCGCGTTGCAAT
1162868 TTTAAGTTTC
Statistics
Matches: 57, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
38 10 0.18
39 1 0.02
40 46 0.81
ACGTcount: A:0.21, C:0.21, G:0.24, T:0.35
Consensus pattern (39 bp):
CGTTGCGATAGTCAATTCGCGTTGCAATAGTCAAATTCG
Found at i:1162855 original size:20 final size:20
Alignment explanation
Indices: 1162761--1162856 Score: 138
Period size: 20 Copynumber: 4.8 Consensus size: 20
1162751 GCGATTCTCT
**
1162761 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCATTTTCG
* **
1162781 CGTTGCAATAGTCAAATTCG
1 CGTTGCGATAGTCATTTTCG
1162801 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
*
1162821 CGCTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
1162841 CGTTGCGATAGTCATT
1 CGTTGCGATAGTCATT
1162857 CGTGTTGCAA
Statistics
Matches: 70, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 70 1.00
ACGTcount: A:0.21, C:0.21, G:0.24, T:0.34
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:1163453 original size:42 final size:42
Alignment explanation
Indices: 1163381--1163463 Score: 105
Period size: 42 Copynumber: 2.0 Consensus size: 42
1163371 CCTCCCCTAT
*
1163381 CGTTCAAGAGGCCCTTATCATCCCTCAAGA-GTCCCCTCCCAC
1 CGTTCAAGAGGCCATTATCATCCCTCAAGAGGT-CCCTCCCAC
* ** *
1163423 CGTTCAAGAGGCCATTGTCATCGTTGAAGAGGTCCCTCCCA
1 CGTTCAAGAGGCCATTATCATCCCTCAAGAGGTCCCTCCCA
1163464 ACATTCTAGA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
42 33 0.94
43 2 0.06
ACGTcount: A:0.22, C:0.36, G:0.19, T:0.23
Consensus pattern (42 bp):
CGTTCAAGAGGCCATTATCATCCCTCAAGAGGTCCCTCCCAC
Found at i:1164895 original size:14 final size:14
Alignment explanation
Indices: 1164858--1164919 Score: 61
Period size: 14 Copynumber: 4.3 Consensus size: 14
1164848 TTGCTTGTTT
*
1164858 AATTGATTTATAAA
1 AATTGATTTGTAAA
1164872 AATTGATTTGTAAA
1 AATTGATTTGTAAA
* *
1164886 AGTTGATTTGTTTAA
1 AATTGATTTG-TAAA
* *
1164901 TATTGATGTGTAAA
1 AATTGATTTGTAAA
1164915 TAATT
1 -AATT
1164920 CTTATTTGTG
Statistics
Matches: 38, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
14 25 0.66
15 13 0.34
ACGTcount: A:0.39, C:0.00, G:0.15, T:0.47
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:1165071 original size:20 final size:20
Alignment explanation
Indices: 1165018--1165071 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
1165008 AGGTACACTT
* **
1165018 TCGCAACGCTAAACTCAAAA
1 TCGCAACGCGAAAGACAAAA
*
1165038 TCGCAATGCGAAAGACAAAA
1 TCGCAACGCGAAAGACAAAA
1165058 TCGCAACGCGAAAG
1 TCGCAACGCGAAAG
1165072 TCAATTCGCG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.44, C:0.26, G:0.19, T:0.11
Consensus pattern (20 bp):
TCGCAACGCGAAAGACAAAA
Found at i:1165163 original size:20 final size:20
Alignment explanation
Indices: 1165136--1165378 Score: 165
Period size: 20 Copynumber: 12.8 Consensus size: 20
1165126 CAAATACCCA
1165136 TTGCGATAATCAAATTCGCG
1 TTGCGATAATCAAATTCGCG
*
1165156 TTAG-GATACTCAAATTCGCG
1 TT-GCGATAATCAAATTCGCG
* *
1165176 TTGCGATAGTCAAATTCGCA
1 TTGCGATAATCAAATTCGCG
* * *
1165196 TTGCGAT--T----TACTCA
1 TTGCGATAATCAAATTCGCG
* * *
1165210 TTGCGCTAGTCAAA-TAGCCG
1 TTGCGATAATCAAATTCG-CG
1165230 TTGCGATAATCAAATTCGCG
1 TTGCGATAATCAAATTCGCG
*
1165250 TTGCGATAGTCAAATTCGCG
1 TTGCGATAATCAAATTCGCG
1165270 TTGCGATAGA-CAAATTCGCG
1 TTGCGATA-ATCAAATTCGCG
* *
1165290 TTGC---AAT---TTTTGCG
1 TTGCGATAATCAAATTCGCG
* * * *
1165304 TTACGATAGTCATATTCGTG
1 TTGCGATAATCAAATTCGCG
** *
1165324 TTATGATAGTCAAATTCGCG
1 TTGCGATAATCAAATTCGCG
*
1165344 TTGCGATAGTCAAATTCGCG
1 TTGCGATAATCAAATTCGCG
*
1165364 TTGCGATATTCAAAT
1 TTGCGATAATCAAAT
1165379 GAATGTGTAA
Statistics
Matches: 177, Mismatches: 28, Indels: 36
0.73 0.12 0.15
Matches are distributed among these distances:
14 18 0.10
16 2 0.01
17 3 0.02
18 1 0.01
19 1 0.01
20 149 0.84
21 3 0.02
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.33
Consensus pattern (20 bp):
TTGCGATAATCAAATTCGCG
Found at i:1165200 original size:94 final size:94
Alignment explanation
Indices: 1165065--1165378 Score: 373
Period size: 94 Copynumber: 3.4 Consensus size: 94
1165055 AAATCGCAAC
* * * * * *
1165065 GCGAAAGTC-AATTCGCGTTACGATAGTCTAATACGCTTTGCGATTTTCTCGTTTCGATAGTCAA
1 GCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCATTGCGATTTTCTCGTTACGATAGTCAA
*
1165129 ATACCCATTGCGATAATCAAATTCGCGTT
66 ATACCCGTTGCGATAATCAAATTCGCGTT
* * * * *
1165158 AG-GATACTCAAATTCGCGTTGCGATAGTCAAATTCGCATTGCGATTTACTCATTGCGCTAGTCA
1 -GCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCATTGCGATTTTCTCGTTACGATAGTCA
*
1165222 AATAGCCGTTGCGATAATCAAATTCGCGTT
65 AATACCCGTTGCGATAATCAAATTCGCGTT
* * *
1165252 GCGATAGTCAAATTCGCGTTGCGATAGACAAATTCGCGTTGCAATTTT-TGCGTTACGATAGTCA
1 GCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCATTGCGATTTTCT-CGTTACGATAGTCA
* * ** ** *
1165316 TATTCGTGTTATGATAGTCAAATTCGCGTT
65 AATACCCGTTGCGATAATCAAATTCGCGTT
*
1165346 GCGATAGTCAAATTCGCGTTGCGATATTCAAAT
1 GCGATAGTCAAATTCGCGTTGCGATAGTCAAAT
1165379 GAATGTGTAA
Statistics
Matches: 187, Mismatches: 30, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
93 7 0.04
94 180 0.96
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33
Consensus pattern (94 bp):
GCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCATTGCGATTTTCTCGTTACGATAGTCAA
ATACCCGTTGCGATAATCAAATTCGCGTT
Found at i:1165223 original size:74 final size:74
Alignment explanation
Indices: 1165134--1165276 Score: 209
Period size: 74 Copynumber: 1.9 Consensus size: 74
1165124 GTCAAATACC
* *
1165134 CATTGCGATAATCAAAT-TCGCGTTAG-GATACTCAAATTCGCGTTGCGATAGTCAAATTCGCAT
1 CATTGCGATAATCAAATAGC-CGTT-GCGATAATCAAATTCGCGTTGCGATAGTCAAATTCGCAT
1165197 TGCGATTTACT
64 TGCGATTTACT
* * *
1165208 CATTGCGCTAGTCAAATAGCCGTTGCGATAATCAAATTCGCGTTGCGATAGTCAAATTCGCGTTG
1 CATTGCGATAATCAAATAGCCGTTGCGATAATCAAATTCGCGTTGCGATAGTCAAATTCGCATTG
1165273 CGAT
66 CGAT
1165277 AGACAAATTC
Statistics
Matches: 62, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
73 1 0.02
74 60 0.97
75 1 0.02
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.31
Consensus pattern (74 bp):
CATTGCGATAATCAAATAGCCGTTGCGATAATCAAATTCGCGTTGCGATAGTCAAATTCGCATTG
CGATTTACT
Found at i:1165311 original size:74 final size:72
Alignment explanation
Indices: 1165153--1165367 Score: 225
Period size: 74 Copynumber: 2.9 Consensus size: 72
1165143 AATCAAATTC
* * * ** **
1165153 GCGTTAGGATACTCAAATTCGCGTTGCGATAGTCAAATTCGCATTGCGATTTACTCATT-GCGCT
1 GCGTTACGATAATCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATAGACAAATTCGCG-T
*
1165217 AGTCAAATA
65 TG-CAAATA
*
1165226 GCCGTTGCGATAATCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATAGACAAATTCGCGT
1 G-CGTTACGATAATCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATAGACAAATTCGCGT
* *
1165291 TGCAATTTTT
65 TGCAA--ATA
* * * ** *
1165301 GCGTTACGATAGTCATATTCGTGTTATGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTT
1 GCGTTACGATAATCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATAGACAAATTCGCGTT
1165366 GC
66 GC
1165368 GATATTCAAA
Statistics
Matches: 120, Mismatches: 18, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
73 4 0.03
74 111 0.93
75 5 0.04
ACGTcount: A:0.26, C:0.20, G:0.22, T:0.33
Consensus pattern (72 bp):
GCGTTACGATAATCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATAGACAAATTCGCGTT
GCAAATA
Found at i:1165605 original size:140 final size:140
Alignment explanation
Indices: 1165349--1165618 Score: 513
Period size: 140 Copynumber: 1.9 Consensus size: 140
1165339 TCGCGTTGCG
1165349 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACATATCA
1 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACATATCA
*
1165414 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
66 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATATTAAAAGTTTACACATAA
1165479 AATACACATA
131 AATACACATA
1165489 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACATATCA
1 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACATATCA
* *
1165554 TAGCAATGTTCAAACTCAAGTTACTAATACATGTCTAACTGAAAATATTAAAAGTTTATACATAA
66 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATATTAAAAGTTTACACATAA
1165619 TACAACGTTT
Statistics
Matches: 127, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
140 127 1.00
ACGTcount: A:0.43, C:0.15, G:0.13, T:0.30
Consensus pattern (140 bp):
ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACATATCA
TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATATTAAAAGTTTACACATAA
AATACACATA
Found at i:1165701 original size:18 final size:18
Alignment explanation
Indices: 1165678--1165712 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1165668 AAGCCGGTTG
*
1165678 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
1165696 TGATTGCGATTTTGATT
1 TGATTGCGATTTTGATT
1165713 GCCTTTTTCT
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:0.17, C:0.03, G:0.26, T:0.54
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:1167768 original size:14 final size:14
Alignment explanation
Indices: 1167749--1167785 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
1167739 TCCCGTGGCA
1167749 TTTTCTTCGGGGAC
1 TTTTCTTCGGGGAC
*
1167763 TTTTCTTCGGGGAT
1 TTTTCTTCGGGGAC
1167777 TTCTTCTTC
1 TT-TTCTTC
1167786 TTCTTTTTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 15 0.71
15 6 0.29
ACGTcount: A:0.05, C:0.22, G:0.22, T:0.51
Consensus pattern (14 bp):
TTTTCTTCGGGGAC
Found at i:1168009 original size:24 final size:24
Alignment explanation
Indices: 1167975--1168028 Score: 99
Period size: 24 Copynumber: 2.2 Consensus size: 24
1167965 CTGAAAAATC
1167975 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
*
1167999 ATCAAAGTCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
1168023 ATCAAA
1 ATCAAA
1168029 TTTCGAATAC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.43, C:0.20, G:0.17, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:1168936 original size:20 final size:20
Alignment explanation
Indices: 1168850--1168936 Score: 129
Period size: 20 Copynumber: 4.3 Consensus size: 20
1168840 AAATTCAGTG
* *
1168850 TTGCGACAGTCAGAATCGCG
1 TTGCGATAGTCAGAATCGCA
* *
1168870 TTGCGACAGTCAGAATCGCG
1 TTGCGATAGTCAGAATCGCA
1168890 TTGCGATAGTCAGAATCGCA
1 TTGCGATAGTCAGAATCGCA
*
1168910 TTGCGATAGTCATAATCGCA
1 TTGCGATAGTCAGAATCGCA
1168930 TTGCGAT
1 TTGCGAT
1168937 TTACATATTC
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 64 1.00
ACGTcount: A:0.26, C:0.22, G:0.26, T:0.25
Consensus pattern (20 bp):
TTGCGATAGTCAGAATCGCA
Found at i:1168936 original size:40 final size:41
Alignment explanation
Indices: 1168850--1169037 Score: 129
Period size: 40 Copynumber: 4.6 Consensus size: 41
1168840 AAATTCAGTG
* * * * *
1168850 TTGCGACAGTCAGAATCGCGTTGCGACAGT-CAGAATCGCG
1 TTGCGATAGTCAGAATCGCATTGCGATAGTACATAATCGCA
1168890 TTGCGATAGTCAGAATCGCATTGCGATAGT-CATAATCGCA
1 TTGCGATAGTCAGAATCGCATTGCGATAGTACATAATCGCA
* * * * *
1168930 TTGCGAT-TTACATATTCGCA-TGCGAT-TTACATATTCGCA
1 TTGCGATAGT-CAGAATCGCATTGCGATAGTACATAATCGCA
* ** * *
1168969 TTGCGATAGTCGGAAAATCGCAACGCGAATTTGGA-A-AATCGCA
1 TTGCGATAGTC--AGAATCGCATTGCG-A-TAGTACATAATCGCA
* *
1169012 ATGCGATAGTCAGAATCGCGTTGCGA
1 TTGCGATAGTCAGAATCGCATTGCGA
1169038 ATCTGGAAAC
Statistics
Matches: 117, Mismatches: 22, Indels: 18
0.75 0.14 0.11
Matches are distributed among these distances:
38 1 0.01
39 24 0.21
40 52 0.44
41 17 0.15
42 3 0.03
43 17 0.15
44 2 0.02
45 1 0.01
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.26
Consensus pattern (41 bp):
TTGCGATAGTCAGAATCGCATTGCGATAGTACATAATCGCA
Found at i:1168955 original size:19 final size:20
Alignment explanation
Indices: 1168905--1168975 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
1168895 ATAGTCAGAA
* *
1168905 TCGCATTGCGATAGT-CATAA
1 TCGCATTGCGAT-TTACATAT
1168925 TCGCATTGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
1168945 TCGCA-TGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
1168964 TCGCATTGCGAT
1 TCGCATTGCGAT
1168976 AGTCGGAAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 4
0.89 0.04 0.08
Matches are distributed among these distances:
19 20 0.43
20 27 0.57
ACGTcount: A:0.25, C:0.21, G:0.18, T:0.35
Consensus pattern (20 bp):
TCGCATTGCGATTTACATAT
Found at i:1170590 original size:29 final size:28
Alignment explanation
Indices: 1170503--1170625 Score: 96
Period size: 29 Copynumber: 4.4 Consensus size: 28
1170493 GACCTTTTCA
* *
1170503 TGTAATTTATAAAAATTATAGGTA-TTAT
1 TGTAATTTATAAAAGTT-TTGGTATTTAT
* * *
1170531 TGTAATTTATGAGAAGTTTT-TTCTTTGAT
1 TGTAATTTAT-AAAAGTTTTGGTATTT-AT
1170560 TGTAATTTATAAATAGTTTTGGTATTTAT
1 TGTAATTTATAAA-AGTTTTGGTATTTAT
*
1170589 TGTAATATTA-AAAAG--TTGACT-TTTAT
1 TGTAAT-TTATAAAAGTTTTG-GTATTTAT
1170615 TGTAATTTATA
1 TGTAATTTATA
1170626 TAAATATTTA
Statistics
Matches: 78, Mismatches: 9, Indels: 18
0.74 0.09 0.17
Matches are distributed among these distances:
25 3 0.04
26 15 0.19
27 2 0.03
28 17 0.22
29 34 0.44
30 7 0.09
ACGTcount: A:0.34, C:0.02, G:0.13, T:0.51
Consensus pattern (28 bp):
TGTAATTTATAAAAGTTTTGGTATTTAT
Found at i:1170683 original size:22 final size:22
Alignment explanation
Indices: 1170640--1170685 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
1170630 TATTTAAAAA
**
1170640 TTTTATTGTAATTTTATATATT
1 TTTTATTGTAATAATATATATT
* *
1170662 TTTTATTTTAATAATATTTATT
1 TTTTATTGTAATAATATATATT
1170684 TT
1 TT
1170686 AGAAATTTAC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTTATTGTAATAATATATATT
Found at i:1174907 original size:31 final size:31
Alignment explanation
Indices: 1174835--1174898 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
1174825 AAGATAGAGG
1174835 TAAATCAGAGAAAAAATGTATTATGATTTTC
1 TAAATCAGAGAAAAAATGTATTATGATTTTC
1174866 TAAATCAGAGAAAAAATGTATTATGATTTTC
1 TAAATCAGAGAAAAAATGTATTATGATTTTC
1174897 TA
1 TA
1174899 TCATAGAGAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.45, C:0.06, G:0.12, T:0.36
Consensus pattern (31 bp):
TAAATCAGAGAAAAAATGTATTATGATTTTC
Found at i:1181433 original size:27 final size:27
Alignment explanation
Indices: 1181389--1181443 Score: 85
Period size: 27 Copynumber: 2.0 Consensus size: 27
1181379 GGGGCTTGGA
1181389 GGTACTTTGGGTCATTTTACACTTCAAG
1 GGTACTTTGGGTCATTTTACACTT-AAG
*
1181417 GGTA-TTTTGGTCATTTTACACTTAAG
1 GGTACTTTGGGTCATTTTACACTTAAG
1181443 G
1 G
1181444 TGAAATTTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
26 4 0.15
27 18 0.69
28 4 0.15
ACGTcount: A:0.22, C:0.15, G:0.22, T:0.42
Consensus pattern (27 bp):
GGTACTTTGGGTCATTTTACACTTAAG
Found at i:1183157 original size:30 final size:31
Alignment explanation
Indices: 1183121--1183180 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
1183111 ATAAATGAAG
*
1183121 AAAATAT-TAAATTTCAGAAA-AGAAAATAAT
1 AAAATATAAAAATTTCA-AAATAGAAAATAAT
*
1183151 AAAATATAAAAATTTTAAAATAGAAAATAA
1 AAAATATAAAAATTTCAAAATAGAAAATAA
1183181 AAATAAAACA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 10 0.38
31 16 0.62
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.27
Consensus pattern (31 bp):
AAAATATAAAAATTTCAAAATAGAAAATAAT
Found at i:1183477 original size:19 final size:19
Alignment explanation
Indices: 1183451--1183494 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
1183441 GTTGTTTTTA
*
1183451 AAAT-AAAAGATAAGAATT
1 AAATAAAAAGAAAAGAATT
*
1183469 AAATAAAAAGAAAATAATT
1 AAATAAAAAGAAAAGAATT
1183488 AAATAAA
1 AAATAAA
1183495 TAATTTAATG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 4 0.17
19 19 0.83
ACGTcount: A:0.73, C:0.00, G:0.07, T:0.20
Consensus pattern (19 bp):
AAATAAAAAGAAAAGAATT
Found at i:1184597 original size:16 final size:16
Alignment explanation
Indices: 1184578--1184608 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
1184568 GAAGAAATAA
1184578 AAATAAATAAATGAAT
1 AAATAAATAAATGAAT
1184594 AAATAAATAAATGAA
1 AAATAAATAAATGAA
1184609 AAGAAAAAAT
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:0.71, C:0.00, G:0.06, T:0.23
Consensus pattern (16 bp):
AAATAAATAAATGAAT
Found at i:1184698 original size:28 final size:27
Alignment explanation
Indices: 1184646--1184700 Score: 65
Period size: 28 Copynumber: 1.9 Consensus size: 27
1184636 CGAAAAATAC
*
1184646 TTTCAAAACCATATATTATATATATGT
1 TTTCAAAACCATATATAATATATATGT
*
1184673 TTTCAAAAACTATACTATAATAATATAT
1 TTTC-AAAACCATA-TATAAT-ATATAT
1184701 ACAATAAGCC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
27 4 0.17
28 8 0.35
29 5 0.22
30 6 0.26
ACGTcount: A:0.45, C:0.11, G:0.02, T:0.42
Consensus pattern (27 bp):
TTTCAAAACCATATATAATATATATGT
Found at i:1190756 original size:18 final size:18
Alignment explanation
Indices: 1190733--1190778 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
1190723 ACCGGTCATA
1190733 ACCCGACCCGA-CAAGTTG
1 ACCCGACCCGACCAA-TTG
* *
1190751 ACCCGACCCAACCCATTG
1 ACCCGACCCGACCAATTG
1190769 ACCCGACCCG
1 ACCCGACCCG
1190779 TTGACCCGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 22 0.92
19 2 0.08
ACGTcount: A:0.26, C:0.48, G:0.17, T:0.09
Consensus pattern (18 bp):
ACCCGACCCGACCAATTG
Found at i:1190784 original size:8 final size:8
Alignment explanation
Indices: 1190773--1190813 Score: 50
Period size: 8 Copynumber: 5.4 Consensus size: 8
1190763 CCATTGACCC
1190773 GACCCGTT
1 GACCCGTT
1190781 GACCCGTT
1 GACCCGTT
1190789 GA-CCGTT
1 GACCCGTT
* *
1190796 TACTCGTT
1 GACCCGTT
1190804 GA-CCGTT
1 GACCCGTT
1190811 GAC
1 GAC
1190814 AGGCGTTGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
7 12 0.44
8 15 0.56
ACGTcount: A:0.15, C:0.32, G:0.24, T:0.29
Consensus pattern (8 bp):
GACCCGTT
Found at i:1193313 original size:12 final size:12
Alignment explanation
Indices: 1193298--1193367 Score: 70
Period size: 12 Copynumber: 5.8 Consensus size: 12
1193288 GATACATTAC
1193298 CTGAATTCTGTT
1 CTGAATTCTGTT
* *
1193310 CTGATTTCTGAT
1 CTGAATTCTGTT
*
1193322 CTGGATTCTGTT
1 CTGAATTCTGTT
*
1193334 CTG-ATATCTGAT
1 CTGAAT-TCTGTT
1193346 CTGAATTCTGTT
1 CTGAATTCTGTT
* *
1193358 TTGATTTCTG
1 CTGAATTCTG
1193368 ATATCTCCGT
Statistics
Matches: 47, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
11 2 0.04
12 43 0.91
13 2 0.04
ACGTcount: A:0.16, C:0.16, G:0.19, T:0.50
Consensus pattern (12 bp):
CTGAATTCTGTT
Found at i:1193329 original size:24 final size:24
Alignment explanation
Indices: 1193298--1193369 Score: 117
Period size: 24 Copynumber: 3.0 Consensus size: 24
1193288 GATACATTAC
1193298 CTGAATTCTGTTCTGATTTCTGAT
1 CTGAATTCTGTTCTGATTTCTGAT
* *
1193322 CTGGATTCTGTTCTGATATCTGAT
1 CTGAATTCTGTTCTGATTTCTGAT
*
1193346 CTGAATTCTGTTTTGATTTCTGAT
1 CTGAATTCTGTTCTGATTTCTGAT
1193370 ATCTCCGTTT
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 43 1.00
ACGTcount: A:0.17, C:0.15, G:0.18, T:0.50
Consensus pattern (24 bp):
CTGAATTCTGTTCTGATTTCTGAT
Found at i:1193336 original size:48 final size:49
Alignment explanation
Indices: 1193261--1193369 Score: 134
Period size: 48 Copynumber: 2.3 Consensus size: 49
1193251 AAATATTTTA
* * *
1193261 TCTGATTTCCGA-CTTGAGTTCTATTCTGATA-CATTACCTGAATTCTGT
1 TCTGATTTCTGATCTGGAGTTCTATTCTGATATC-TGACCTGAATTCTGT
* *
1193309 TCTGATTTCTGATCTGGA-TTCTGTTCTGATATCTGATCTGAATTCTGT
1 TCTGATTTCTGATCTGGAGTTCTATTCTGATATCTGACCTGAATTCTGT
*
1193357 TTTGATTTCTGAT
1 TCTGATTTCTGAT
1193370 ATCTCCGTTT
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
48 48 0.91
49 5 0.09
ACGTcount: A:0.18, C:0.17, G:0.17, T:0.48
Consensus pattern (49 bp):
TCTGATTTCTGATCTGGAGTTCTATTCTGATATCTGACCTGAATTCTGT
Found at i:1198003 original size:12 final size:12
Alignment explanation
Indices: 1197988--1198057 Score: 54
Period size: 12 Copynumber: 5.8 Consensus size: 12
1197978 GATACATTAC
1197988 CTGAATTCTGTT
1 CTGAATTCTGTT
* *
1198000 CTGATTTCTGAT
1 CTGAATTCTGTT
*
1198012 CTGGATTCTGTT
1 CTGAATTCTGTT
1198024 CTGATATT-T-TAT
1 CTGA-ATTCTGT-T
*
1198036 CTAAATTCTGTT
1 CTGAATTCTGTT
* *
1198048 TTGATTTCTG
1 CTGAATTCTG
1198058 ATATCTCCGT
Statistics
Matches: 44, Mismatches: 10, Indels: 8
0.71 0.16 0.13
Matches are distributed among these distances:
11 4 0.09
12 36 0.82
13 4 0.09
ACGTcount: A:0.17, C:0.14, G:0.16, T:0.53
Consensus pattern (12 bp):
CTGAATTCTGTT
Found at i:1198007 original size:48 final size:48
Alignment explanation
Indices: 1197951--1198059 Score: 148
Period size: 48 Copynumber: 2.3 Consensus size: 48
1197941 AAATATTTTA
*
1197951 TCTGATTTCTGA-CTTGAATTCTGTTCTGATACATTACCTGAATTCTGT
1 TCTGATTTCTGATC-TGAATTCTGTTCTGATACATTACCTAAATTCTGT
* ** *
1197999 TCTGATTTCTGATCTGGATTCTGTTCTGATATTTTATCTAAATTCTGT
1 TCTGATTTCTGATCTGAATTCTGTTCTGATACATTACCTAAATTCTGT
*
1198047 TTTGATTTCTGAT
1 TCTGATTTCTGAT
1198060 ATCTCCGTTT
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
48 53 0.98
49 1 0.02
ACGTcount: A:0.19, C:0.16, G:0.15, T:0.50
Consensus pattern (48 bp):
TCTGATTTCTGATCTGAATTCTGTTCTGATACATTACCTAAATTCTGT
Found at i:1198019 original size:24 final size:24
Alignment explanation
Indices: 1197951--1198059 Score: 107
Period size: 24 Copynumber: 4.5 Consensus size: 24
1197941 AAATATTTTA
1197951 TCTGATTTCTGA-CTTGAATTCTGT
1 TCTGATTTCTGATC-TGAATTCTGT
* * *
1197975 TCTGA-TACATTACCTGAATTCTGT
1 TCTGATTTC-TGATCTGAATTCTGT
*
1197999 TCTGATTTCTGATCTGGATTCTGT
1 TCTGATTTCTGATCTGAATTCTGT
* *
1198023 TCTGATATT-TTATCTAAATTCTGT
1 TCTGAT-TTCTGATCTGAATTCTGT
*
1198047 TTTGATTTCTGAT
1 TCTGATTTCTGAT
1198060 ATCTCCGTTT
Statistics
Matches: 69, Mismatches: 11, Indels: 10
0.77 0.12 0.11
Matches are distributed among these distances:
23 4 0.06
24 60 0.87
25 5 0.07
ACGTcount: A:0.19, C:0.16, G:0.15, T:0.50
Consensus pattern (24 bp):
TCTGATTTCTGATCTGAATTCTGT
Found at i:1200194 original size:6 final size:6
Alignment explanation
Indices: 1200183--1200217 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
1200173 CTTAATTACG
1200183 AAAATT AAAATT AAAATT AAAATT AAAATT AAAAT
1 AAAATT AAAATT AAAATT AAAATT AAAATT AAAAT
1200218 ATTCGATTCG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (6 bp):
AAAATT
Found at i:1200410 original size:24 final size:24
Alignment explanation
Indices: 1200383--1200435 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
1200373 TAAATTTTAG
* * *
1200383 AAAATATAAAAAA-ATATTAAAAT
1 AAAAAATAAAAAATAAAATAAAAT
1200406 AAAAAATAAAAAATAAAATAAAAT
1 AAAAAATAAAAAATAAAATAAAAT
1200430 AAAAAA
1 AAAAAA
1200436 GAGAAGTGGG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 12 0.46
24 14 0.54
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (24 bp):
AAAAAATAAAAAATAAAATAAAAT
Found at i:1200418 original size:14 final size:15
Alignment explanation
Indices: 1200391--1200434 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
1200381 AGAAAATATA
*
1200391 AAAAAATATTAAAAT
1 AAAAAATATAAAAAT
1200406 AAAAAATA-AAAAAT
1 AAAAAATATAAAAAT
*
1200420 AAAATAAAATAAAAA
1 AAAA-AATATAAAAA
1200435 AGAGAAGTGG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 9 0.36
15 11 0.44
16 5 0.20
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (15 bp):
AAAAAATATAAAAAT
Found at i:1200435 original size:19 final size:21
Alignment explanation
Indices: 1200388--1200435 Score: 66
Period size: 19 Copynumber: 2.4 Consensus size: 21
1200378 TTTAGAAAAT
1200388 ATAAAAAAATATTAAAATAAA
1 ATAAAAAAATATTAAAATAAA
1200409 A-AATAAAAA-A-TAAAATAAA
1 ATAA-AAAAATATTAAAATAAA
1200428 ATAAAAAA
1 ATAAAAAA
1200436 GAGAAGTGGG
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
19 14 0.56
20 5 0.20
21 6 0.24
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (21 bp):
ATAAAAAAATATTAAAATAAA
Found at i:1209995 original size:16 final size:16
Alignment explanation
Indices: 1209969--1210045 Score: 71
Period size: 15 Copynumber: 5.2 Consensus size: 16
1209959 CCTTAAGAAA
1209969 GAAAAAT-AAGAAAAAT
1 GAAAAATGAAG-AAAAT
1209985 -AAAAATGAAGAAAAT
1 GAAAAATGAAGAAAAT
1210000 GAAAAATG-A-AAAA-
1 GAAAAATGAAGAAAAT
1210013 GAAAAA-GAA-AAAAT
1 GAAAAATGAAGAAAAT
* *
1210027 GAAAAAAG-AGAAAAG
1 GAAAAATGAAGAAAAT
1210042 GAAA
1 GAAA
1210046 GAAAAAAATA
Statistics
Matches: 54, Mismatches: 1, Indels: 13
0.79 0.01 0.19
Matches are distributed among these distances:
12 1 0.02
13 11 0.20
14 11 0.20
15 21 0.39
16 10 0.19
ACGTcount: A:0.75, C:0.00, G:0.17, T:0.08
Consensus pattern (16 bp):
GAAAAATGAAGAAAAT
Found at i:1210005 original size:7 final size:7
Alignment explanation
Indices: 1209978--1210032 Score: 62
Period size: 7 Copynumber: 7.9 Consensus size: 7
1209968 AGAAAAATAA
1209978 GAAAAAT
1 GAAAAAT
1209985 -AAAAAT
1 GAAAAAT
1209991 GAAGAAAAT
1 G-A-AAAAT
1210000 GAAAAAT
1 GAAAAAT
1210007 GAAAAA-
1 GAAAAAT
1210013 GAAAAA-
1 GAAAAAT
1210019 GAAAAAAT
1 G-AAAAAT
1210027 GAAAAA
1 GAAAAA
1210033 AGAGAAAAGG
Statistics
Matches: 43, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
6 13 0.30
7 21 0.49
8 3 0.07
9 6 0.14
ACGTcount: A:0.76, C:0.00, G:0.15, T:0.09
Consensus pattern (7 bp):
GAAAAAT
Found at i:1210017 original size:35 final size:35
Alignment explanation
Indices: 1209976--1210058 Score: 100
Period size: 35 Copynumber: 2.4 Consensus size: 35
1209966 AAAGAAAAAT
*
1209976 AAGAAAAATAAAAATGAAGAAAATGA-AAAATGAAA-
1 AAGAAAAATAAAAATGAA-AAAA-GAGAAAAGGAAAG
*
1210011 AAGAAAAAGAAAAAATGAAAAAAGAGAAAAGGAAAG
1 AAGAAAAA-TAAAAATGAAAAAAGAGAAAAGGAAAG
1210047 AA-AAAAATAAAA
1 AAGAAAAATAAAA
1210059 TAAATATAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
34 6 0.14
35 25 0.60
36 11 0.26
ACGTcount: A:0.77, C:0.00, G:0.16, T:0.07
Consensus pattern (35 bp):
AAGAAAAATAAAAATGAAAAAAGAGAAAAGGAAAG
Found at i:1210024 original size:20 final size:19
Alignment explanation
Indices: 1209976--1210032 Score: 66
Period size: 16 Copynumber: 3.1 Consensus size: 19
1209966 AAAGAAAAAT
*
1209976 AAGAAAAATAAAAATG---
1 AAGAAAAAGAAAAATGAAA
*
1209992 AAGAAAATGAAAAATGAAA
1 AAGAAAAAGAAAAATGAAA
1210011 AAGAAAAAGAAAAAATGAAA
1 AAGAAAAAG-AAAAATGAAA
1210031 AA
1 AA
1210033 AGAGAAAAGG
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
16 14 0.41
19 8 0.24
20 12 0.35
ACGTcount: A:0.77, C:0.00, G:0.14, T:0.09
Consensus pattern (19 bp):
AAGAAAAAGAAAAATGAAA
Found at i:1210032 original size:27 final size:27
Alignment explanation
Indices: 1209969--1210052 Score: 89
Period size: 27 Copynumber: 3.0 Consensus size: 27
1209959 CCTTAAGAAA
*
1209969 GAAAAATAAGAAAAATAAAAATGAAGAAAAT
1 GAAAAAT--GAAAAAGAAAAA-GAA-AAAAT
1210000 GAAAAATGAAAAAGAAAAAGAAAAAAT
1 GAAAAATGAAAAAGAAAAAGAAAAAAT
* *
1210027 GAAAAAAGAGAAAAG-GAAAGAAAAAA
1 GAAAAATGA-AAAAGAAAAAGAAAAAA
1210053 ATAAAATAAA
Statistics
Matches: 49, Mismatches: 3, Indels: 6
0.84 0.05 0.10
Matches are distributed among these distances:
27 23 0.47
28 8 0.16
29 11 0.22
31 7 0.14
ACGTcount: A:0.76, C:0.00, G:0.17, T:0.07
Consensus pattern (27 bp):
GAAAAATGAAAAAGAAAAAGAAAAAAT
Found at i:1210040 original size:7 final size:7
Alignment explanation
Indices: 1209966--1210041 Score: 50
Period size: 7 Copynumber: 10.6 Consensus size: 7
1209956 TTGCCTTAAG
1209966 AAAGAAA
1 AAAGAAA
1209973 AATA-AGAA
1 AA-AGA-AA
*
1209981 AAATAAA
1 AAAGAAA
*
1209988 AATGAAGA
1 AAAGAA-A
1209996 AAATGAAA
1 AAA-GAAA
*
1210004 AATG-AA
1 AAAGAAA
1210010 AAAG-AA
1 AAAGAAA
1210016 AAAGAAA
1 AAAGAAA
1210023 AAATGAAA
1 AAA-GAAA
*
1210031 AAAGAGA
1 AAAGAAA
1210038 AAAG
1 AAAG
1210042 GAAAGAAAAA
Statistics
Matches: 56, Mismatches: 6, Indels: 14
0.74 0.08 0.18
Matches are distributed among these distances:
6 11 0.20
7 23 0.41
8 19 0.34
9 3 0.05
ACGTcount: A:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (7 bp):
AAAGAAA
Found at i:1211483 original size:135 final size:135
Alignment explanation
Indices: 1211275--1211611 Score: 390
Period size: 135 Copynumber: 2.5 Consensus size: 135
1211265 ATCAAACTCA
* * * *
1211275 ATTCAATCTTCCC-GAGGAACAGTGGAATAAATCAACATCTCCAGATTTGATTCTCCCTGAAGAA
1 ATTCAATCTTCCCTGAAGAACAGTGGAATGAATCAACGTCTCCAGATCTGATTCTCCCTGAAGAA
* * * * * * ** * * *
1211339 ATAGTGGAACAGATCCCCTATCTTTCTATATTTTATCTTCCCAGAGTATTAGTGGAACACGTCTT
66 ACAGCGGAACAAATCCCCTATCTTTCCAAACTTTATCTTCCCAGAGTAGCAGTCGAACAAGTCTA
* *
1211404 CTTTG
131 CCTCG
* * *
1211409 ATTCAATCTTCCCTAAAGAACAGTGGAATGAATCAACGTCTCCAGATCTGATTTTCCCTGACGAA
1 ATTCAATCTTCCCTGAAGAACAGTGGAATGAATCAACGTCTCCAGATCTGATTCTCCCTGAAGAA
* * *
1211474 ACAGCGGAACAAATCCCCTTTGTTTCCAAACTTTATCTTCCCTGAGTAGCAGTCGAACAAGTCTA
66 ACAGCGGAACAAATCCCCTATCTTTCCAAACTTTATCTTCCCAGAGTAGCAGTCGAACAAGTCTA
1211539 CCTCG
131 CCTCG
* * * * * *
1211544 ATTCAATCTTCCATGAAGAACAGTGGAATGAATCGATGTTTCTAGATCTGA-TCTACCCTAAAGA
1 ATTCAATCTTCCCTGAAGAACAGTGGAATGAATCAACGTCTCCAGATCTGATTCT-CCCTGAAGA
1211608 AACA
65 AACA
1211612 ATGGAGCATA
Statistics
Matches: 169, Mismatches: 32, Indels: 3
0.83 0.16 0.01
Matches are distributed among these distances:
134 15 0.09
135 154 0.91
ACGTcount: A:0.31, C:0.24, G:0.16, T:0.30
Consensus pattern (135 bp):
ATTCAATCTTCCCTGAAGAACAGTGGAATGAATCAACGTCTCCAGATCTGATTCTCCCTGAAGAA
ACAGCGGAACAAATCCCCTATCTTTCCAAACTTTATCTTCCCAGAGTAGCAGTCGAACAAGTCTA
CCTCG
Found at i:1212831 original size:20 final size:20
Alignment explanation
Indices: 1212806--1212858 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
1212796 ATAATATACA
1212806 AGTATCGATACTAGGTTAGT
1 AGTATCGATACTAGGTTAGT
1212826 AGTATCGATACTAGGTTAGT
1 AGTATCGATACTAGGTTAGT
*
1212846 AGTACCGATACTA
1 AGTATCGATACTA
1212859 TGGAGCCTAG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.32, C:0.13, G:0.23, T:0.32
Consensus pattern (20 bp):
AGTATCGATACTAGGTTAGT
Found at i:1213301 original size:46 final size:46
Alignment explanation
Indices: 1213224--1213479 Score: 386
Period size: 46 Copynumber: 5.6 Consensus size: 46
1213214 AGTTTTAGAG
*
1213224 CATAATTAAAATGCATGAAATGATGCATTAAGGCATGAAAGGATGC
1 CATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
* * * * *
1213270 CACAACTAATATGCATGAAAGGATACATTAAGGCATGAAAGGATAC
1 CATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
* * *
1213316 CATAATTAAAATCCATGAAAGGATGCATTAAGGCTTGAAAAGATGC
1 CATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
1213362 CATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
1 CATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
* * * *
1213408 CATAATTAAAATGAATGAAACGATGCATTAAGGTATGAAAGGATAC
1 CATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
*
1213454 CATAACTAAAATGCATGAAAGGATGC
1 CATAATTAAAATGCATGAAAGGATGC
1213480 CATAACTAAA
Statistics
Matches: 186, Mismatches: 24, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 186 1.00
ACGTcount: A:0.45, C:0.12, G:0.21, T:0.22
Consensus pattern (46 bp):
CATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
Found at i:1213307 original size:20 final size:20
Alignment explanation
Indices: 1213236--1213405 Score: 72
Period size: 20 Copynumber: 7.6 Consensus size: 20
1213226 TAATTAAAAT
* *
1213236 GCATGAAATGATGCATTAAG
1 GCATGAAAGGATACATTAAG
* *
1213256 GCATGAAAGGATGCCACAACTAATAT
1 GCATGAAAGGAT---AC-A-TTA-AG
1213282 GCATGAAAGGATACATTAAG
1 GCATGAAAGGATACATTAAG
*
1213302 GCATGAAAGGATACCATAATTAAAAT
1 GCATGAAAGGATA-C---ATT--AAG
* *
1213328 CCATGAAAGGATGCATTAAG
1 GCATGAAAGGATACATTAAG
* *
1213348 GCTTGAAAAGATGCCATA-ATTAAAAT
1 GCATG-AAAG--G--ATACATT--AAG
*
1213374 GCATGAAAGGATGCATTAAG
1 GCATGAAAGGATACATTAAG
1213394 GCATGAAAGGAT
1 GCATGAAAGGAT
1213406 GCCATAATTA
Statistics
Matches: 113, Mismatches: 17, Indels: 40
0.66 0.10 0.24
Matches are distributed among these distances:
20 44 0.39
21 9 0.08
22 7 0.06
23 5 0.04
24 7 0.06
25 9 0.08
26 32 0.28
ACGTcount: A:0.44, C:0.12, G:0.22, T:0.22
Consensus pattern (20 bp):
GCATGAAAGGATACATTAAG
Found at i:1213426 original size:26 final size:26
Alignment explanation
Indices: 1213394--1213538 Score: 116
Period size: 26 Copynumber: 6.0 Consensus size: 26
1213384 ATGCATTAAG
1213394 GCATGAAAGGATGCCATAATTAAAAT
1 GCATGAAAGGATGCCATAATTAAAAT
* * *
1213420 GAATGAAACGATG-C---ATT--AAG
1 GCATGAAAGGATGCCATAATTAAAAT
* * *
1213440 GTATGAAAGGATACCATAACTAAAAT
1 GCATGAAAGGATGCCATAATTAAAAT
*
1213466 GCATGAAAGGATGCCATAACTAAAAT
1 GCATGAAAGGATGCCATAATTAAAAT
* *
1213492 GCATGGAAGGATG-C---ATT--AAG
1 GCATGAAAGGATGCCATAATTAAAAT
*
1213512 GCATGAAAGGATGCCATAATTTAAAT
1 GCATGAAAGGATGCCATAATTAAAAT
1213538 G
1 G
1213539 TATAAATGGA
Statistics
Matches: 92, Mismatches: 15, Indels: 24
0.70 0.11 0.18
Matches are distributed among these distances:
20 26 0.28
21 2 0.02
22 5 0.05
24 5 0.05
25 2 0.02
26 52 0.57
ACGTcount: A:0.44, C:0.12, G:0.22, T:0.22
Consensus pattern (26 bp):
GCATGAAAGGATGCCATAATTAAAAT
Found at i:1213550 original size:72 final size:72
Alignment explanation
Indices: 1213256--1213530 Score: 234
Period size: 72 Copynumber: 3.9 Consensus size: 72
1213246 ATGCATTAAG
* * * * *
1213256 GCATGAAAGGATGCCACAACTAATATGCATGAAAGGATACATTAAGGCATGAAAGGATACCATAA
1 GCATGAAAGGATGCCATAACTAAAATGAATGAAACGATGCATTAAGGCATGAAAGGATACCATAA
*
1213321 TTAAAAT
66 CTAAAAT
* * * *
1213328 CCATGAAAGGATG-CATTAAGGCTTGAAAA-G-ATG---CCAT-AATTAAAATGCATGAAAGGAT
1 GCATGAAAGGATGCCA-TAA--C-T-AAAATGAATGAAACGATGCATT--AAGGCATGAAAGGAT
* *
1213386 -GCAT---T--AAG
59 ACCATAACTAAAAT
* *
1213394 GCATGAAAGGATGCCATAATTAAAATGAATGAAACGATGCATTAAGGTATGAAAGGATACCATAA
1 GCATGAAAGGATGCCATAACTAAAATGAATGAAACGATGCATTAAGGCATGAAAGGATACCATAA
1213459 CTAAAAT
66 CTAAAAT
* * * *
1213466 GCATGAAAGGATGCCATAACTAAAATGCATGGAAGGATGCATTAAGGCATGAAAGGATGCCATAA
1 GCATGAAAGGATGCCATAACTAAAATGAATGAAACGATGCATTAAGGCATGAAAGGATACCATAA
1213531 TTTAAATGTA
Statistics
Matches: 160, Mismatches: 23, Indels: 40
0.72 0.10 0.18
Matches are distributed among these distances:
62 4 0.03
63 2 0.01
64 3 0.02
66 30 0.19
67 8 0.05
68 4 0.03
70 4 0.03
71 7 0.04
72 89 0.56
74 4 0.03
75 2 0.01
76 3 0.02
ACGTcount: A:0.44, C:0.13, G:0.22, T:0.21
Consensus pattern (72 bp):
GCATGAAAGGATGCCATAACTAAAATGAATGAAACGATGCATTAAGGCATGAAAGGATACCATAA
CTAAAAT
Found at i:1214091 original size:3 final size:3
Alignment explanation
Indices: 1214083--1214116 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
1214073 GAGTGTTACA
* *
1214083 ATT ATT ATT ATT ACT ATT ATT GTT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1214117 ATGTAATTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:1215223 original size:387 final size:383
Alignment explanation
Indices: 1214513--1215278 Score: 1392
Period size: 387 Copynumber: 2.0 Consensus size: 383
1214503 CAAAAAAATA
1214513 AAAAAAAAGAGATCTGTAAACGAGGGTTATAAAACCCAAGAATATTGTAAGGATAGAGGTTTCTC
1 AAAAAAAAGAGATCTGTAAACGAGGGTTATAAAACCCAAGAATATTGTAAGGATAGAGGTTTCTC
1214578 CCCTTTCGGGTTTTTTTCCTAAAAAGCAATACAAGCAAAAAAAACGTAAACATTCGAATGTATAT
66 CCCTTTCGGGTTTTTTTCCTAAAAAGCAATACAAGCAAAAAAAACGTAAACATTCGAATGTATAT
*
1214643 TTTTTGGTATTTTTTTTCAATTTCAAAACAAATAAAAAAGAAATAAAAATCTTTGAATGAAACAA
131 TTTTTGGTATTTTTTTTCAATTTCAAAACAAATAAAAAAGAAATAAAAAGCTTTGAATGAAACAA
* **
1214708 TAAACAAGGGAATGGAGCAGATCTAGTTACCTGGGGATAGTCAAACCATACGGTCGGTTCGTATT
196 TAAACAAGGGAATGGAGCAGATCTAGTTACCAGGGGATAGTCAAACCATACGGTCAATTCGTATT
1214773 TGCGGCGGCTGGAGTGTGAGTACCAAAAGGTCAAGGTCTTCTTTTGGGTTGTTTAGAGCCCTTTT
261 TGCGGCGGCTGGAGTGTGAGTACCAAAAGGTCAAGGTCTTCTTTTGGGTTGTTTAGAGCCCTTTT
1214838 AGGTAGTTCTAGCCCTAGATCTAGGCCTGGAGGTGTAGATCTGAGTGATTAGGATGTT
326 AGGTAGTTCTAGCCCTAGATCTAGGCCTGGAGGTGTAGATCTGAGTGATTAGGATGTT
*
1214896 AAAAAAAA-AGATCTGTAAACGAGGGTTATAAAACCCGAGAATATTGTAAGGATAGAGGTTTCTC
1 AAAAAAAAGAGATCTGTAAACGAGGGTTATAAAACCCAAGAATATTGTAAGGATAGAGGTTTCTC
1214960 CCCTTTCGGGTTTTTTTCCTAAAAAGCAATACAAGCAAAAAAAGAAAACAG-AAACATTCGAATG
66 CCCTTTCGGGTTTTTTTCCTAAAAAGCAATACAAGC---AAAA-AAAAC-GTAAACATTCGAATG
*
1215024 TATATTTTTTGGTATTTTTTTTTCAGTTTCAAAACAAATAAAAAAGAAATAAAAAGCTTTGAATG
126 TATATTTTTTGGTA-TTTTTTTTCAATTTCAAAACAAATAAAAAAGAAATAAAAAGCTTTGAATG
1215089 AAACAATAAACAAGGGAATGGAGCAGATCTAGTTACCAGGGGATAGTCAAACCATACGGTCAATT
190 AAACAATAAACAAGGGAATGGAGCAGATCTAGTTACCAGGGGATAGTCAAACCATACGGTCAATT
* *
1215154 CGTCTTTGCGGCGGCTGGAGTGTGAGTACCAAAAGGTCAGGGTCTTCTTTTGGGTTGTTTAGAGC
255 CGTATTTGCGGCGGCTGGAGTGTGAGTACCAAAAGGTCAAGGTCTTCTTTTGGGTTGTTTAGAGC
1215219 CCTTTTAGGTAGTTCTAGCCCTAGATCTAGGCCTGGAGGTGTAGATCTGAGTGATTAGGA
320 CCTTTTAGGTAGTTCTAGCCCTAGATCTAGGCCTGGAGGTGTAGATCTGAGTGATTAGGA
1215279 GGTTTTGGCT
Statistics
Matches: 369, Mismatches: 8, Indels: 8
0.96 0.02 0.02
Matches are distributed among these distances:
382 91 0.25
383 8 0.02
385 4 0.01
386 32 0.09
387 234 0.63
ACGTcount: A:0.34, C:0.14, G:0.22, T:0.29
Consensus pattern (383 bp):
AAAAAAAAGAGATCTGTAAACGAGGGTTATAAAACCCAAGAATATTGTAAGGATAGAGGTTTCTC
CCCTTTCGGGTTTTTTTCCTAAAAAGCAATACAAGCAAAAAAAACGTAAACATTCGAATGTATAT
TTTTTGGTATTTTTTTTCAATTTCAAAACAAATAAAAAAGAAATAAAAAGCTTTGAATGAAACAA
TAAACAAGGGAATGGAGCAGATCTAGTTACCAGGGGATAGTCAAACCATACGGTCAATTCGTATT
TGCGGCGGCTGGAGTGTGAGTACCAAAAGGTCAAGGTCTTCTTTTGGGTTGTTTAGAGCCCTTTT
AGGTAGTTCTAGCCCTAGATCTAGGCCTGGAGGTGTAGATCTGAGTGATTAGGATGTT
Found at i:1216596 original size:131 final size:131
Alignment explanation
Indices: 1216324--1216659 Score: 446
Period size: 131 Copynumber: 2.6 Consensus size: 131
1216314 ATTTCAGTTG
*
1216324 GAGTAATAAATGATTACTTAAAGGCATGAGAGGTCATTTATTCTCGATTGGAAATAATTAGATA-
1 GAGTAATAAATGATTACTTTAAGGCATGAGAGGTCATTTATTCTCGATTGGAAATAATTAGATAT
** * * * *
1216388 TATAGTTTTCTTTTGAATCAATATTGAATTTTAAGACGAAATAGTAATATCTTATCATTTCGGTC
66 TATAGTTTTCACTCGAATCAATATTGAATTTTAAGACGAAAGAGCAATATCTTATCATTTCGATC
*
1216453 G
131 A
* * * *
1216454 GAGTAATAAATGATTGCTTTAAGACATGAGAGGTCATTTATTCTCGATTGGAAATCATTAGACAT
1 GAGTAATAAATGATTACTTTAAGGCATGAGAGGTCATTTATTCTCGATTGGAAATAATTAGATAT
* * *
1216519 TATCA-TTTTCACTCGAATCAATATTTAATTTTAAGAC-AAAGGGGCGATATCTCT-TCATTTCG
66 TAT-AGTTTTCACTCGAATCAATATTGAATTTTAAGACGAAA-GAGCAATATCT-TATCATTTCG
1216581 ATCA
128 ATCA
* * * *
1216585 GAGTAATAAATGACTACTTTAAGGCATGAAAGGTCATTTATTATCAATTGGAAATAATTAGATAT
1 GAGTAATAAATGATTACTTTAAGGCATGAGAGGTCATTTATTCTCGATTGGAAATAATTAGATAT
1216650 TATAGTTTTC
66 TATAGTTTTC
1216660 GTTCTAAAAT
Statistics
Matches: 178, Mismatches: 23, Indels: 9
0.85 0.11 0.04
Matches are distributed among these distances:
130 63 0.35
131 113 0.63
132 2 0.01
ACGTcount: A:0.35, C:0.11, G:0.16, T:0.37
Consensus pattern (131 bp):
GAGTAATAAATGATTACTTTAAGGCATGAGAGGTCATTTATTCTCGATTGGAAATAATTAGATAT
TATAGTTTTCACTCGAATCAATATTGAATTTTAAGACGAAAGAGCAATATCTTATCATTTCGATC
A
Found at i:1217400 original size:2 final size:2
Alignment explanation
Indices: 1217393--1217422 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1217383 GTTTTCAATT
*
1217393 TA TA TA TA TA TA TA TA TA TA TA TA AA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1217423 AAATTATTCT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:1219177 original size:19 final size:20
Alignment explanation
Indices: 1219141--1219178 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
1219131 GGTTTTATGA
**
1219141 AAGTTAAAAAGGTTTTTTTT
1 AAGTTAAAAAGGGGTTTTTT
1219161 AAGTT-AAAAGGGGTTTTT
1 AAGTTAAAAAGGGGTTTTT
1219179 GGAAAAATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 11 0.69
20 5 0.31
ACGTcount: A:0.34, C:0.00, G:0.21, T:0.45
Consensus pattern (20 bp):
AAGTTAAAAAGGGGTTTTTT
Found at i:1219177 original size:20 final size:20
Alignment explanation
Indices: 1219141--1219178 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1219131 GGTTTTATGA
*
1219141 AAGTTAAAAAGGTTTTTTTT
1 AAGTTAAAAAGGGTTTTTTT
*
1219161 AAGTTAAAAGGGGTTTTT
1 AAGTTAAAAAGGGTTTTT
1219179 GGAAAAATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.34, C:0.00, G:0.21, T:0.45
Consensus pattern (20 bp):
AAGTTAAAAAGGGTTTTTTT
Found at i:1221428 original size:14 final size:14
Alignment explanation
Indices: 1221411--1221437 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1221401 TTTTGAGTCA
1221411 TTTATTTTTTTAGT
1 TTTATTTTTTTAGT
1221425 TTTATTTTTTTAG
1 TTTATTTTTTTAG
1221438 AATAAATGTA
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:0.15, C:0.00, G:0.07, T:0.78
Consensus pattern (14 bp):
TTTATTTTTTTAGT
Found at i:1227358 original size:21 final size:21
Alignment explanation
Indices: 1227332--1227381 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
1227322 TCTCCTGTGC
1227332 ATTTATTTATTATTT-ATTATT
1 ATTTATTTATTATTTCATTA-T
*
1227353 ATTTATATATTATTTCATTAT
1 ATTTATTTATTATTTCATTAT
1227374 ATTTATTT
1 ATTTATTT
1227382 TGATATGGGA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
21 22 0.85
22 4 0.15
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (21 bp):
ATTTATTTATTATTTCATTAT
Found at i:1227412 original size:6 final size:6
Alignment explanation
Indices: 1227401--1228648 Score: 2316
Period size: 6 Copynumber: 210.0 Consensus size: 6
1227391 ATAGATTATC
1227401 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT
1 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT
1227449 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT
1 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT
1227497 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT
1 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT
1227545 ATG--T ATGTAT ATGTAT ATGTAT ATGTAT ATG--T ATGTAT ATGTAT
1 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT
1227589 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT
1 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT
1227637 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT
1 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT
1227685 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT
1 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT
1227733 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT
1 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT
1227781 ATGTAT ATGTAT ATGTATAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT
1 ATGTAT ATGTAT ATG--TAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT
1227831 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT
1 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT
1227879 ATGTAT ATGTAT A--TAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT
1 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT
1227925 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT
1 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT
1227973 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT
1 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT
1228021 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATG--T
1 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT
1228067 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT
1 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT
1228115 ATGTAT ATGTAT ATGTAT ATGTATGT ATGTATGT ATGTAT ATGTAT ATGTAT
1 ATGTAT ATGTAT ATGTAT ATGTA--T ATGTA--T ATGTAT ATGTAT ATGTAT
1228167 ATGTAT ATG--T ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT
1 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT
1228213 ATG--T ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT
1 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT
1228259 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT
1 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT
1228307 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT
1 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT
1228355 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT
1 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT
1228403 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATG--T ATGTAT ATGTAT
1 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT
1228449 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATG--T
1 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT
1228495 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATG--T ATGTAT
1 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT
1228541 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT
1 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT
1228589 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT
1 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT
1228637 ATGTAT ATGTAT
1 ATGTAT ATGTAT
1228649 CCTCATCTTC
Statistics
Matches: 1220, Mismatches: 0, Indels: 44
0.97 0.00 0.03
Matches are distributed among these distances:
4 36 0.03
6 1164 0.95
8 20 0.02
ACGTcount: A:0.33, C:0.00, G:0.17, T:0.50
Consensus pattern (6 bp):
ATGTAT
Found at i:1233953 original size:3 final size:3
Alignment explanation
Indices: 1233945--1233993 Score: 91
Period size: 3 Copynumber: 16.7 Consensus size: 3
1233935 AAATATCTCG
1233945 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1233992 TT
1 TT
1233994 TGTATTTATA
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 43 0.96
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1237205 original size:12 final size:12
Alignment explanation
Indices: 1237187--1237219 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
1237177 TGTACATTTT
1237187 CTCTGATTTCTG
1 CTCTGATTTCTG
*
1237199 TTCTGATTTCTG
1 CTCTGATTTCTG
1237211 CTCTGATTT
1 CTCTGATTT
1237220 TTTATATTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.09, C:0.21, G:0.15, T:0.55
Consensus pattern (12 bp):
CTCTGATTTCTG
Found at i:1248441 original size:33 final size:32
Alignment explanation
Indices: 1248401--1248476 Score: 82
Period size: 33 Copynumber: 2.3 Consensus size: 32
1248391 CCATGGCTTG
* *
1248401 CTTTCTTTTTAAATTTTTCTTTTTCTTTTATTTT
1 CTTTCTTTTT-AATTTTTC-TCTTCTTATATTTT
* *
1248435 C-TTCTTTTCTGATTTTTCTCTTCTTATCTTTT
1 CTTTCTTTT-TAATTTTTCTCTTCTTATATTTT
1248467 CTTTCTTTTT
1 CTTTCTTTTT
1248477 GCACTCCAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
32 13 0.36
33 21 0.58
34 2 0.06
ACGTcount: A:0.08, C:0.17, G:0.01, T:0.74
Consensus pattern (32 bp):
CTTTCTTTTTAATTTTTCTCTTCTTATATTTT
Found at i:1263655 original size:178 final size:180
Alignment explanation
Indices: 1263355--1263732 Score: 590
Period size: 178 Copynumber: 2.1 Consensus size: 180
1263345 TTTTCTAATT
* *
1263355 TATATAA-ATTAAATA-TTTTTAATTCAAAAAAGTTTATAATTAATTTAAATAATAAATAATTAT
1 TATATAATATTTAATATTTTTTAATTCAAAAAAGTTTACAATTAATTTAAATAAT-AATAATTAT
* * *
1263418 AAAATAAACATTTTATATAAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTATTGGA
65 AAAATAAAAAATTTATATAAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTATTAGA
*
1263483 TCTTAAATTATTAATTGGG-TTTTAGATGGTTTGGGCTT-AGCCCATATGTTA
130 TCTTAAATTATTAATTGGGTTTTTA-ATGATTTGGG-TTGAGCCCATATGTTA
1263534 TATATAATATTTAATATTTTTTAATT-AAAAACAGTTTACAATTAATTTAAATAAT-ATAATTAT
1 TATATAATATTTAATATTTTTTAATTCAAAAA-AGTTTACAATTAATTTAAATAATAATAATTAT
1263597 AAAATAAAAAATTTATAT-AATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTATTAGA
65 AAAATAAAAAATTTATATAAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTATTAGA
*
1263661 TCTTAAATTATTAATTGGGTTTTTAATGATTTGGGTTGAGCCCATTTGTTA
130 TCTTAAATTATTAATTGGGTTTTTAATGATTTGGGTTGAGCCCATATGTTA
1263712 TATATAATATATTTAATATTT
1 TATAT-A-ATATTTAATATTT
1263733 AAAATTTAAT
Statistics
Matches: 185, Mismatches: 7, Indels: 13
0.90 0.03 0.06
Matches are distributed among these distances:
177 2 0.01
178 90 0.49
179 37 0.20
180 25 0.14
181 31 0.17
ACGTcount: A:0.41, C:0.03, G:0.08, T:0.47
Consensus pattern (180 bp):
TATATAATATTTAATATTTTTTAATTCAAAAAAGTTTACAATTAATTTAAATAATAATAATTATA
AAATAAAAAATTTATATAAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTATTAGAT
CTTAAATTATTAATTGGGTTTTTAATGATTTGGGTTGAGCCCATATGTTA
Found at i:1264526 original size:2 final size:2
Alignment explanation
Indices: 1264519--1264545 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1264509 CTTACTTACG
1264519 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
1264546 AGTAATCATA
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:1268764 original size:21 final size:21
Alignment explanation
Indices: 1268715--1268778 Score: 92
Period size: 21 Copynumber: 3.0 Consensus size: 21
1268705 CATATGAAAT
*
1268715 TTGTCCCGAAGGACCTGTGAA
1 TTGTCCCGAAGGACCTATGAA
*
1268736 TATGTCCCGAAGGACCTATGAG
1 T-TGTCCCGAAGGACCTATGAA
*
1268758 TTGTCCCAAAGGACCTATGAA
1 TTGTCCCGAAGGACCTATGAA
1268779 ACCCTCGACT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
21 19 0.50
22 19 0.50
ACGTcount: A:0.28, C:0.23, G:0.25, T:0.23
Consensus pattern (21 bp):
TTGTCCCGAAGGACCTATGAA
Found at i:1269074 original size:14 final size:15
Alignment explanation
Indices: 1269047--1269075 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1269037 ATATCATATA
1269047 TCTTATGTTTTATGC
1 TCTTATGTTTTATGC
1269062 TCTTATG-TTTATGC
1 TCTTATGTTTTATGC
1269076 ATATCATGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.14, C:0.14, G:0.14, T:0.59
Consensus pattern (15 bp):
TCTTATGTTTTATGC
Found at i:1273295 original size:90 final size:92
Alignment explanation
Indices: 1273138--1273335 Score: 285
Period size: 90 Copynumber: 2.2 Consensus size: 92
1273128 TCAGAACTGC
* * * * *
1273138 GTCCGTAGGGCTTACCCTCAGCACACAGCAAAAGAGGAGCCAACCTAAGGATATGCCTTGGGACC
1 GTCCGTAGGGCTTACCATAAGAACACAACAAAAGAGAAGCCAACCTAAGGATATGCCTTGGGACC
*
1273203 TAT-AGGCCTACCCAAGGGTATCCTTTG
66 TATGA-GCCTACCCAAGGGTATCCTTAG
*
1273230 GTCCGTAGGGCTTACCATAAGAACACAAC-AAAG-GAAGCCAACCTAAGGATATGCCTTGGGGCC
1 GTCCGTAGGGCTTACCATAAGAACACAACAAAAGAGAAGCCAACCTAAGGATATGCCTTGGGACC
1273293 TATGAGCCTACCCAAGGGTATCCTTAG
66 TATGAGCCTACCCAAGGGTATCCTTAG
*
1273320 GTCCGTAAGGACTTAC
1 GTCCGT-AGGGCTTAC
1273336 TAGCTGGATC
Statistics
Matches: 96, Mismatches: 8, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
90 58 0.60
91 13 0.14
92 25 0.26
ACGTcount: A:0.29, C:0.27, G:0.25, T:0.20
Consensus pattern (92 bp):
GTCCGTAGGGCTTACCATAAGAACACAACAAAAGAGAAGCCAACCTAAGGATATGCCTTGGGACC
TATGAGCCTACCCAAGGGTATCCTTAG
Found at i:1279296 original size:15 final size:15
Alignment explanation
Indices: 1279276--1279365 Score: 162
Period size: 15 Copynumber: 6.0 Consensus size: 15
1279266 TAATAAGGTT
1279276 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
1279291 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
*
1279306 ATTTATTATAAAATA
1 ATTTATTTTAAAATA
1279321 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
*
1279336 ATTTATTATAAAATA
1 ATTTATTTTAAAATA
1279351 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
1279366 TGGATTGATT
Statistics
Matches: 71, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 71 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
ATTTATTTTAAAATA
Found at i:1279330 original size:45 final size:45
Alignment explanation
Indices: 1279276--1279434 Score: 169
Period size: 45 Copynumber: 3.3 Consensus size: 45
1279266 TAATAAGGTT
1279276 ATTTATTTTAAAATAATTTATTTTAAAATAATTTATTATAAAATA
1 ATTTATTTTAAAATAATTTATTTTAAAATAATTTATTATAAAATA
* *
1279321 ATTTATTTTAAAATAATTTATTATAAAATAATTTATTTTAAAATATGGA
1 ATTTATTTTAAAATAATTTATTTTAAAATAATTTATTAT-AAA-AT--A
* *
1279370 TTGATTTATTTTAAAA-ATATTTATTTT-AAATAATTTATTAGTATGAATTG
1 ---ATTTATTTTAAAATA-ATTTATTTTAAAATAATTTATTA-TA--AAATA
1279420 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
1279435 TGGATTGATT
Statistics
Matches: 96, Mismatches: 6, Indels: 21
0.78 0.05 0.17
Matches are distributed among these distances:
45 37 0.39
46 3 0.03
47 15 0.16
48 1 0.01
49 1 0.01
51 14 0.15
52 23 0.24
53 2 0.02
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.52
Consensus pattern (45 bp):
ATTTATTTTAAAATAATTTATTTTAAAATAATTTATTATAAAATA
Found at i:1279376 original size:22 final size:22
Alignment explanation
Indices: 1279351--1279453 Score: 98
Period size: 22 Copynumber: 4.5 Consensus size: 22
1279341 TTATAAAATA
1279351 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
** *
1279373 ATTTATTTTAAAAATATTTATTTT
1 ATTTATTTT-AAAATATGGA-TTG
** * * * *
1279397 AAATAATTTATTAGTATGAATTG
1 ATTTATTTTA-AAATATGGATTG
1279420 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
1279442 ATTTATTTTAAA
1 ATTTATTTTAAA
1279454 TAATTTATTA
Statistics
Matches: 61, Mismatches: 17, Indels: 6
0.73 0.20 0.07
Matches are distributed among these distances:
22 30 0.49
23 18 0.30
24 13 0.21
ACGTcount: A:0.39, C:0.00, G:0.09, T:0.52
Consensus pattern (22 bp):
ATTTATTTTAAAATATGGATTG
Found at i:1279426 original size:32 final size:32
Alignment explanation
Indices: 1279388--1279705 Score: 188
Period size: 32 Copynumber: 10.4 Consensus size: 32
1279378 TTTTAAAAAT
*
1279388 ATTTATTTTAAATAATTTATTAGTATGAATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
1279420 ATTTA-TTT---TAA---A--A-TATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
1279442 ATTTATTTTAAATAATTTATTAGTATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
* ** * *
1279474 ATTTATTTTAAAATATGGATTTATTTA-TTTTAAATA
1 ATTTATTTT-AAATA---ATTTA-TTAGTATGGATTG
* * * *
1279510 ATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
1 ATTTATT--T-T-AAATAATTTA--TT--AGTATGGATTG
*
1279550 ATTTA--TT--AT--TCTAGTT-GTATGGATTG
1 ATTTATTTTAAATAATTTA-TTAGTATGGATTG
1279576 ATTTATTTTAAATAATTTATTAGTATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
*
1279608 ATTTATTTTAAATAATTTATCAGTATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
* *
1279640 AATTA-TTT---TAA---ACTA-T-T-GATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
1279662 ATTTATTTTAAATAATTTATTAGTATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
1279694 ATTTATTTTAAA
1 ATTTATTTTAAA
1279706 ATATGGATTG
Statistics
Matches: 221, Mismatches: 26, Indels: 78
0.68 0.08 0.24
Matches are distributed among these distances:
22 22 0.10
23 8 0.04
24 1 0.00
25 3 0.01
26 20 0.09
28 8 0.04
29 6 0.03
30 6 0.03
31 10 0.05
32 89 0.40
33 5 0.02
35 1 0.00
36 22 0.10
37 6 0.03
38 1 0.00
39 4 0.02
40 9 0.04
ACGTcount: A:0.35, C:0.01, G:0.12, T:0.53
Consensus pattern (32 bp):
ATTTATTTTAAATAATTTATTAGTATGGATTG
Found at i:1279443 original size:69 final size:67
Alignment explanation
Indices: 1279306--1279462 Score: 221
Period size: 69 Copynumber: 2.3 Consensus size: 67
1279296 TTTTAAAATA
*
1279306 ATTTATTAT-AAAATAATTTATTTTAAAATAATTTATTATAAAATAATTTATTTTAAAATATGGA
1 ATTTATTTTAAAAAT-ATTTATTTTAAAATAATTTATTATAAAATAATTTATTTTAAAATATGGA
1279370 TTG
65 TTG
* *
1279373 ATTTATTTTAAAAATATTTATTTT-AAATAATTTATTAGTATGAATTGATTTATTTTAAAATATG
1 ATTTATTTTAAAAATATTTATTTTAAAATAATTTATTA-TA--AAATAATTTATTTTAAAATATG
1279437 GATTG
63 GATTG
*
1279442 ATTTATTTTAAATA-ATTTATT
1 ATTTATTTTAAAAATATTTATT
1279463 AGTATGGATT
Statistics
Matches: 82, Mismatches: 4, Indels: 7
0.88 0.04 0.08
Matches are distributed among these distances:
66 13 0.16
67 19 0.23
68 12 0.15
69 38 0.46
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (67 bp):
ATTTATTTTAAAAATATTTATTTTAAAATAATTTATTATAAAATAATTTATTTTAAAATATGGAT
TG
Found at i:1279453 original size:54 final size:54
Alignment explanation
Indices: 1279388--1279903 Score: 514
Period size: 54 Copynumber: 9.4 Consensus size: 54
1279378 TTTTAAAAAT
*
1279388 ATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
*
1279442 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTT
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
1279496 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
*
1279550 ATTTA--TT--AT--TCTAGTT-GTATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTG
1 ATTTATTTTAAATAATTTA-TTAGTATGGATTGATTTA-TTT---TAA---A--A-TATGGATTG
* * * *
1279608 ATTTATTTTAAATAATTTATCAGTATGGATTGAATTATTTTAAACTATTGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
1279662 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
* * *
1279716 ATTTA--TT--AT--TGTAGTT-GTATGGATTGATTTATTTTAAATAATTTAATAGTATGG
1 ATTTATTTTAAATAATTTA-TTAGTATGGATTGATTTATTTT-AA-AA--T-AT-GGATTG
* * *
1279770 ATTGA-TTT--AT--TTTA-AAATATGGATTGATTTATTTTAAATAATTTATTAGTATGTATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTT-AA-AA--TA-T-G---G-ATTG
*
1279828 ATTTATTTTAAATAATTTATTTGTATGGATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
1279882 ATTTATTTTAAATAATTTATTA
1 ATTTATTTTAAATAATTTATTA
1279904 TTGTAGTTGT
Statistics
Matches: 397, Mismatches: 27, Indels: 76
0.79 0.05 0.15
Matches are distributed among these distances:
48 40 0.10
49 9 0.02
50 6 0.02
52 8 0.02
53 3 0.01
54 236 0.59
55 9 0.02
57 2 0.01
58 22 0.06
59 4 0.01
60 7 0.02
61 2 0.01
62 4 0.01
63 10 0.03
64 35 0.09
ACGTcount: A:0.34, C:0.01, G:0.12, T:0.53
Consensus pattern (54 bp):
ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
Found at i:1279490 original size:22 final size:22
Alignment explanation
Indices: 1279465--1279507 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
1279455 AATTTATTAG
1279465 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
*
1279487 TATGGATTTATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
1279508 TAATTTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:1279531 original size:18 final size:18
Alignment explanation
Indices: 1279510--1279557 Score: 51
Period size: 22 Copynumber: 2.4 Consensus size: 18
1279500 ATTTTAAATA
*
1279510 ATTTATTAGTATGGATTG
1 ATTTATTAATATGGATTG
1279528 ATTTATTTTAAAATATGGATTG
1 ATTTA--TT--AATATGGATTG
1279550 ATTTATTA
1 ATTTATTA
1279558 TTCTAGTTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 8
0.74 0.03 0.24
Matches are distributed among these distances:
18 6 0.24
20 4 0.16
22 15 0.60
ACGTcount: A:0.33, C:0.00, G:0.15, T:0.52
Consensus pattern (18 bp):
ATTTATTAATATGGATTG
Found at i:1279606 original size:166 final size:166
Alignment explanation
Indices: 1279433--1279888 Score: 702
Period size: 166 Copynumber: 2.7 Consensus size: 166
1279423 TATTTTAAAA
* *
1279433 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTTAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGAATTATTTTAAAATATGGATTGAT
1279498 TTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTCTA
66 TTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTCTA
*
1279563 GTTGTATGGATTGATTTATTTTAAATAATTTATTAG
131 GTTGTATGGATTGATTTATTTTAAATAATTTAATAG
* * *
1279599 TATGGATTGATTTATTTTAAATAATTTATCAGTATGGATTGAATTATTTTAAACTATTGATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGAATTATTTTAAAATATGGATTGAT
*
1279664 TTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTGTA
66 TTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTCTA
1279729 GTTGTATGGATTGATTTATTTTAAATAATTTAATAG
131 GTTGTATGGATTGATTTATTTTAAATAATTTAATAG
** ** * * * * * *
1279765 TATGGATTGATTTATTTTAAA-ATATGGATT-G-ATTTATTTTAAATAATTTATTAGTATGTATT
1 TATGGATTGATTTATTTTAAATA-ATTTATTAGTATGGA-TTGAATTATTTTA-AAATATGGATT
*
1279827 GATTTATTTTAAATAATTTATTTGTATGGATTGATTTATTTTAAAATATGGATTGATTTATT
63 GATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATT
1279889 TTAAATAATT
Statistics
Matches: 267, Mismatches: 20, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
164 3 0.01
165 12 0.04
166 252 0.94
ACGTcount: A:0.33, C:0.01, G:0.13, T:0.53
Consensus pattern (166 bp):
TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGAATTATTTTAAAATATGGATTGAT
TTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTCTA
GTTGTATGGATTGATTTATTTTAAATAATTTAATAG
Found at i:1279618 original size:220 final size:219
Alignment explanation
Indices: 1279388--1279903 Score: 758
Period size: 220 Copynumber: 2.3 Consensus size: 219
1279378 TTTTAAAAAT
*
1279388 ATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTGATTTATTTTAA
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAA
* *
1279453 ATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTTATTTATTTTAAATAATTTA-TT
66 ATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTA--TT--AT--TGTAGTT
* * ***
1279517 AGTATGGATTGATTTATTTT-AA-AA-T-AT-GGATTGATTTA-TTATTCTAGTTGTATGGATTG
125 -GTATGGATTGATTTATTTTAAATAATTAATAGGATGGATTGATTTATTCTA-AAATATGGATTG
1279576 ATTTATTTTAAATAATTTATTAGTATGGATTG
188 ATTTATTTTAAATAATTTATTAGTATGGATTG
* * * *
1279608 ATTTATTTTAAATAATTTATCAGTATGGATTGAATTATTTTAAACTATTGATTGATTTATTTTAA
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAA
1279673 ATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTGTATGG
66 ATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTGTATGG
* *
1279738 ATTGATTTATTTTAAATAATTTAATAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATT
131 ATTGATTTATTTTAAATAA-TTAATAGGATGGATTGATTTATTCTAAAATATGGATTGATTTATT
*
1279803 TTAAATAATTTATTAGTATGTATTG
195 TTAAATAATTTATTAGTATGGATTG
*
1279828 ATTTATTTTAAATAATTTATTTGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAA
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAA
1279893 ATAATTTATTA
66 ATAATTTATTA
1279904 TTGTAGTTGT
Statistics
Matches: 268, Mismatches: 20, Indels: 16
0.88 0.07 0.05
Matches are distributed among these distances:
214 22 0.08
215 4 0.01
216 4 0.01
218 3 0.01
219 2 0.01
220 226 0.84
221 7 0.03
ACGTcount: A:0.34, C:0.01, G:0.12, T:0.53
Consensus pattern (219 bp):
ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAA
ATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTGTATGG
ATTGATTTATTTTAAATAATTAATAGGATGGATTGATTTATTCTAAAATATGGATTGATTTATTT
TAAATAATTTATTAGTATGGATTG
Found at i:1279661 original size:134 final size:136
Alignment explanation
Indices: 1279388--1279839 Score: 430
Period size: 134 Copynumber: 3.3 Consensus size: 136
1279378 TTTTAAAAAT
* * *
1279388 ATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTGATTTATTTTAA
1 ATTTATTTT-AA-AA-TTATTAGGATGGATTGATTTATTCTAAAATATGGATTGATTTATTTTAA
* * * *
1279453 ATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTTAT-TTAT---TTTAAATAATTT
63 ATAATTTATTAGTATGGATTGATTTATTTT-AAATA---ATTTATAGTATGGATTGAATTATTTT
* *
1279514 ATTAGTATGGATTG
124 A-AAATATGGATTG
* * ***
1279528 ATTTATTTTAAAA-TA-T-GGATTGATTTA-TTATTCTAGTTGTATGGATTGATTTATTTTAAAT
1 ATTTATTTTAAAATTATTAGGATGGATTGATTTATTCTA-AAATATGGATTGATTTATTTTAAAT
*
1279589 AATTTATTAGTATGGATTGATTTATTTTAAATAATTTATCAGTATGGATTGAATTATTTTAAACT
65 AATTTATTAGTATGGATTGATTTATTTTAAATAATTTAT-AGTATGGATTGAATTATTTTAAAAT
*
1279654 ATTGATTG
129 ATGGATTG
* *
1279662 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTA--TT--
1 ATTTATTTT-AA-AA-TTATTAGGATGGATTGATTTATTCTAAAATATGGATTGATTTATTTTAA
* *
1279723 AT--TGTAGTT-GTATGGATTGATTTATTTTAAATAATTTAATAGTATGGATTGATTTATTTTAA
63 ATAATTTA-TTAGTATGGATTGATTTATTTTAAATAATTT-ATAGTATGGATTGAATTATTTTAA
1279785 AATATGGATTG
126 AATATGGATTG
* * *
1279796 ATTTATTTTAAATAATTTATTAGTATGTATTGATTTATTTTAAA
1 ATTTATTTT-AA-AA-TTATTAGGATGGATTGATTTATTCTAAA
1279840 TAATTTATTT
Statistics
Matches: 270, Mismatches: 27, Indels: 36
0.81 0.08 0.11
Matches are distributed among these distances:
130 6 0.02
132 3 0.01
133 12 0.04
134 179 0.66
135 17 0.06
136 6 0.02
138 6 0.02
139 3 0.01
140 31 0.11
141 7 0.03
ACGTcount: A:0.34, C:0.01, G:0.13, T:0.52
Consensus pattern (136 bp):
ATTTATTTTAAAATTATTAGGATGGATTGATTTATTCTAAAATATGGATTGATTTATTTTAAATA
ATTTATTAGTATGGATTGATTTATTTTAAATAATTTATAGTATGGATTGAATTATTTTAAAATAT
GGATTG
Found at i:1279699 original size:18 final size:18
Alignment explanation
Indices: 1279676--1279723 Score: 51
Period size: 22 Copynumber: 2.4 Consensus size: 18
1279666 ATTTTAAATA
*
1279676 ATTTATTAGTATGGATTG
1 ATTTATTAATATGGATTG
1279694 ATTTATTTTAAAATATGGATTG
1 ATTTA--TT--AATATGGATTG
1279716 ATTTATTA
1 ATTTATTA
1279724 TTGTAGTTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 8
0.74 0.03 0.24
Matches are distributed among these distances:
18 6 0.24
20 4 0.16
22 15 0.60
ACGTcount: A:0.33, C:0.00, G:0.15, T:0.52
Consensus pattern (18 bp):
ATTTATTAATATGGATTG
Found at i:1279773 original size:32 final size:32
Alignment explanation
Indices: 1279732--1279871 Score: 174
Period size: 32 Copynumber: 4.7 Consensus size: 32
1279722 TATTGTAGTT
1279732 GTATGGATTGATTTATTTTAAATAATTTAATA
1 GTATGGATTGATTTATTTTAAATAATTTAATA
1279764 GTATGGATTGATTTA-TTT---T-A---AA-A
1 GTATGGATTGATTTATTTTAAATAATTTAATA
*
1279787 -TATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTAATA
* * *
1279818 GTATGTATTGATTTATTTTAAATAATTTATTT
1 GTATGGATTGATTTATTTTAAATAATTTAATA
1279850 GTATGGATTGATTTATTTTAAA
1 GTATGGATTGATTTATTTTAAA
1279872 ATATGGATTG
Statistics
Matches: 94, Mismatches: 4, Indels: 20
0.80 0.03 0.17
Matches are distributed among these distances:
22 14 0.15
23 4 0.04
24 2 0.02
26 1 0.01
27 2 0.02
28 1 0.01
30 1 0.01
31 4 0.04
32 65 0.69
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.53
Consensus pattern (32 bp):
GTATGGATTGATTTATTTTAAATAATTTAATA
Found at i:1279790 original size:22 final size:22
Alignment explanation
Indices: 1279765--1279807 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
1279755 AATTTAATAG
1279765 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
1279787 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
1279808 TAATTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:1279867 original size:22 final size:22
Alignment explanation
Indices: 1279851--1279893 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
1279841 AATTTATTTG
1279851 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
1279873 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
1279894 TAATTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:1279953 original size:31 final size:31
Alignment explanation
Indices: 1279918--1279976 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
1279908 AGTTGTATGG
* *
1279918 ATTATTTAAATTTCAGTATTGTAAAACTAAA
1 ATTATTTAAATCTCAGTATTGCAAAACTAAA
1279949 ATTATTTAAATCTCAGTATTGCAAAACT
1 ATTATTTAAATCTCAGTATTGCAAAACT
1279977 CTTTTAAGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.42, C:0.10, G:0.07, T:0.41
Consensus pattern (31 bp):
ATTATTTAAATCTCAGTATTGCAAAACTAAA
Found at i:1280287 original size:24 final size:24
Alignment explanation
Indices: 1280260--1280310 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
1280250 AGTTTTTTAG
1280260 TTTTAACCAAGATGGGTTTCCTAC
1 TTTTAACCAAGATGGGTTTCCTAC
*
1280284 TTTTAACCAAGATGTGTTTCCTAC
1 TTTTAACCAAGATGGGTTTCCTAC
1280308 TTT
1 TTT
1280311 CTCAATATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.24, C:0.20, G:0.14, T:0.43
Consensus pattern (24 bp):
TTTTAACCAAGATGGGTTTCCTAC
Found at i:1283181 original size:3 final size:3
Alignment explanation
Indices: 1283163--1283219 Score: 55
Period size: 3 Copynumber: 19.3 Consensus size: 3
1283153 TCGTCCCAAC
* * * *
1283163 ATT ATT AGT ATA ATT ATT ATT ATT AAT AGT ATT ATT ATT ATTT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT
1283209 -TT ATT -TT ATT A
1 ATT ATT ATT ATT A
1283220 ATTTTCAGGT
Statistics
Matches: 44, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
2 4 0.09
3 37 0.84
4 3 0.07
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:1283223 original size:14 final size:15
Alignment explanation
Indices: 1283176--1283224 Score: 55
Period size: 18 Copynumber: 3.1 Consensus size: 15
1283166 ATTAGTATAA
1283176 TTATTATTATTAATAGT
1 TTATTATTATTAAT--T
*
1283193 ATTATTATTATTTATT
1 -TTATTATTATTAATT
1283209 TTATT-TTATTAATT
1 TTATTATTATTAATT
1283223 TT
1 TT
1283225 CAGGTTACAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
14 10 0.34
15 5 0.17
16 1 0.03
18 13 0.45
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (15 bp):
TTATTATTATTAATT
Found at i:1285432 original size:132 final size:131
Alignment explanation
Indices: 1285132--1285497 Score: 520
Period size: 132 Copynumber: 2.8 Consensus size: 131
1285122 TCAATATTGA
* * *
1285132 AAATAGTAATATCTTTTCATTTC-AGTTGGAGTAATAAATGATTGCTTTAAGGCATAAGAGGTCA
1 AAATAGTGATATCTCTTCATTTCGA-TTGGAGTAATAAATGACTGCTTTAAGGCATAAGAGGTCA
* * * *
1285196 TTTATTCTCGATTGGAAATAATTAGATATTATCGTTTTCTTTCGAATCAATATTGATTTTTAAGT
65 TTTATTCTCGATTGGAAATAATTAGATATTATCTTTTTCTCTCGAATCAATATTGACTTTTAAGA
1285261 CG
130 CG
* * *
1285263 GAATAGTGATATCTCTTCATTTCGATTGGAGTAATAAAT-AGCTGCTTTAAGGCGTGAGAGGTCA
1 AAATAGTGATATCTCTTCATTTCGATTGGAGTAATAAATGA-CTGCTTTAAGGCATAAGAGGTCA
* *
1285327 TTTATTCTCAATTGGAAATCATTAGATATTATCATTTTTCTCTCGAATCAATATTGACTTTTAAG
65 TTTATTCTCGATTGGAAATAATTAGATATTATC-TTTTTCTCTCGAATCAATATTGACTTTTAAG
1285392 ACG
129 ACG
* * * *
1285395 AAATAGTGATATCTCTTCGTTTCGATCGGAGTAATAAATGACTGCTTTAAGGCATCAGATGTCAT
1 AAATAGTGATATCTCTTCATTTCGATTGGAGTAATAAATGACTGCTTTAAGGCATAAGAGGTCAT
* * *
1285460 TTATTCTTGATTGGAAATAAATAGATATTATCGTTTTC
66 TTATTCTCGATTGGAAATAATTAGATATTATCTTTTTC
1285498 ATTCTTAAAA
Statistics
Matches: 208, Mismatches: 23, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
130 1 0.00
131 90 0.43
132 116 0.56
133 1 0.00
ACGTcount: A:0.31, C:0.12, G:0.17, T:0.40
Consensus pattern (131 bp):
AAATAGTGATATCTCTTCATTTCGATTGGAGTAATAAATGACTGCTTTAAGGCATAAGAGGTCAT
TTATTCTCGATTGGAAATAATTAGATATTATCTTTTTCTCTCGAATCAATATTGACTTTTAAGAC
G
Found at i:1293476 original size:21 final size:22
Alignment explanation
Indices: 1293441--1293522 Score: 89
Period size: 21 Copynumber: 3.8 Consensus size: 22
1293431 TTAGTGCAGA
*
1293441 GGGAATCGA-TCCCCCCTTGA-
1 GGGAACCGATTCCCCCCTTGAG
*
1293461 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATTCCCCCCTTG-AG
*
1293484 GGGAACCGATTCCCCCCAT-AG
1 GGGAACCGATTCCCCCCTTGAG
* *
1293505 GGGAATCGATACCCCCCT
1 GGGAACCGATTCCCCCCT
1293523 GGGGTTCTGG
Statistics
Matches: 52, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
20 8 0.15
21 26 0.50
22 1 0.02
23 17 0.33
ACGTcount: A:0.22, C:0.35, G:0.24, T:0.18
Consensus pattern (22 bp):
GGGAACCGATTCCCCCCTTGAG
Found at i:1305672 original size:7 final size:7
Alignment explanation
Indices: 1305660--1305736 Score: 145
Period size: 7 Copynumber: 10.9 Consensus size: 7
1305650 ATACTTCGCC
1305660 TGAAAAA
1 TGAAAAA
1305667 TGAAAAA
1 TGAAAAA
1305674 TGAAAAA
1 TGAAAAA
1305681 TGAAAAA
1 TGAAAAA
1305688 TGAAAAA
1 TGAAAAA
1305695 TGAAAAA
1 TGAAAAA
1305702 TGAAAAA
1 TGAAAAA
1305709 TGAAAAA
1 TGAAAAA
1305716 TGAAAAA
1 TGAAAAA
1305723 TGAAAAAA
1 TG-AAAAA
1305731 TGAAAA
1 TGAAAA
1305737 GAAAAAGAAA
Statistics
Matches: 69, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
7 62 0.90
8 7 0.10
ACGTcount: A:0.71, C:0.00, G:0.14, T:0.14
Consensus pattern (7 bp):
TGAAAAA
Found at i:1305742 original size:21 final size:20
Alignment explanation
Indices: 1305660--1305746 Score: 124
Period size: 21 Copynumber: 4.2 Consensus size: 20
1305650 ATACTTCGCC
1305660 TGAAAAATGAAAAATGAAAAA
1 TGAAAAATGAAAAA-GAAAAA
1305681 TGAAAAATGAAAAATGAAAAA
1 TGAAAAATGAAAAA-GAAAAA
1305702 TGAAAAATGAAAAATGAAAAA
1 TGAAAAATGAAAAA-GAAAAA
1305723 TGAAAAAATG-AAAAGAAAAA
1 TG-AAAAATGAAAAAGAAAAA
1305743 -GAAA
1 TGAAA
1305747 GAAAAAATGA
Statistics
Matches: 65, Mismatches: 0, Indels: 5
0.93 0.00 0.07
Matches are distributed among these distances:
18 3 0.05
19 1 0.02
20 6 0.09
21 48 0.74
22 7 0.11
ACGTcount: A:0.72, C:0.00, G:0.15, T:0.13
Consensus pattern (20 bp):
TGAAAAATGAAAAAGAAAAA
Found at i:1307191 original size:133 final size:133
Alignment explanation
Indices: 1307031--1307458 Score: 570
Period size: 133 Copynumber: 3.2 Consensus size: 133
1307021 ATTGAACTCG
* *
1307031 ATTCAATCTTCCCTGAGGAACAGTGGAATGAATCAATGTCTCCAGATCTGATTTTCCCTGAAGAA
1 ATTCAATCTTCCCTGAAGAACAGTGGAATGAATCAATATCTCCAGATCTGATTTTCCCTGAAGAA
* * * *
1307096 GCAATGGAATAGATCCCCTCTTTCCAGGTTTGATCTTCCCTGAGTAGCAGTGGAACAAGTCTGCC
66 ACAACGGAACAGATCCCCTCTTTCCAGATTTGATCTTCCCTGAGTAGCAGTGGAACAAGTCTGCC
1307161 TCA
131 TCA
* * * * *
1307164 ATTCAATCTTCCCTGAAGAACAGTGGAATGAATCAACACCTCTAGGTTTGATTTTCCCT-AGAGA
1 ATTCAATCTTCCCTGAAGAACAGTGGAATGAATCAATATCTCCAGATCTGATTTTCCCTGA-AGA
* * * * *
1307228 AACAACGAAACAGATCCCCTCTTTCCATATTTGATCTTCTCTGAGTAGCAATGGAACAAGTCTGT
65 AACAACGGAACAGATCCCCTCTTTCCAGATTTGATCTTCCCTGAGTAGCAGTGGAACAAGTCTGC
1307293 CTCA
130 CTCA
* * * * *
1307297 ATTCAATCTTCCCTGAAGAACAATGGAATGAATCAATATCTCCATACCTGATTTTACCTGGAGAA
1 ATTCAATCTTCCCTGAAGAACAGTGGAATGAATCAATATCTCCAGATCTGATTTTCCCTGAAGAA
* * * * * * *
1307362 ACAGCAGAACATATCCCCTCTTTCCAGATTTGGTCTTTCTTGAGTAGCAGTGGAACAAGTCTTCC
66 ACAACGGAACAGATCCCCTCTTTCCAGATTTGATCTTCCCTGAGTAGCAGTGGAACAAGTCTGCC
*
1307427 TCG
131 TCA
*
1307430 ATTCAATCTTCCATGAAGAACAGTGGAAT
1 ATTCAATCTTCCCTGAAGAACAGTGGAAT
1307459 TATTCCATAT
Statistics
Matches: 252, Mismatches: 41, Indels: 4
0.85 0.14 0.01
Matches are distributed among these distances:
132 1 0.00
133 251 1.00
ACGTcount: A:0.30, C:0.24, G:0.18, T:0.29
Consensus pattern (133 bp):
ATTCAATCTTCCCTGAAGAACAGTGGAATGAATCAATATCTCCAGATCTGATTTTCCCTGAAGAA
ACAACGGAACAGATCCCCTCTTTCCAGATTTGATCTTCCCTGAGTAGCAGTGGAACAAGTCTGCC
TCA
Found at i:1308746 original size:107 final size:108
Alignment explanation
Indices: 1308570--1308766 Score: 242
Period size: 107 Copynumber: 1.8 Consensus size: 108
1308560 TCACCTATAA
* *
1308570 GGATCGAATCTACTATTTACCTATTTTTATGTATGCTTTATAATTTTTGGGAAATTTGATGTTTA
1 GGATCGAATCTACTATTTACCCATTTTTATGGATGCTTTATAATTTTTGGGAAATTTGATGTTTA
* *
1308635 GTCCC-CTGTAGTTTAGCGTTTTTTTTATGTTAGTCACTTGTAG
66 GTCCCTCTAT-GTTTAGCGTGTTTTTTATGTTAGTCACTTGTAG
* * ** *
1308678 GGATCGAA-CTTCTATTTACCCATTTTTATGGATG--TTATATCTTTTTAGGGTTATTTGCT-TC
1 GGATCGAATCTACTATTTACCCATTTTTATGGATGCTTTATA-ATTTTT-GGGAAATTTGATGT-
1308739 TTAGTCCCTCTATGTTTAGCGTGTTTTT
63 TTAGTCCCTCTATGTTTAGCGTGTTTTT
1308767 ATATTTTGGT
Statistics
Matches: 76, Mismatches: 9, Indels: 9
0.81 0.10 0.10
Matches are distributed among these distances:
105 5 0.07
106 6 0.08
107 54 0.71
108 11 0.14
ACGTcount: A:0.19, C:0.14, G:0.17, T:0.50
Consensus pattern (108 bp):
GGATCGAATCTACTATTTACCCATTTTTATGGATGCTTTATAATTTTTGGGAAATTTGATGTTTA
GTCCCTCTATGTTTAGCGTGTTTTTTATGTTAGTCACTTGTAG
Found at i:1309113 original size:17 final size:16
Alignment explanation
Indices: 1309091--1309129 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
1309081 GATGATTTTA
*
1309091 CTATTTATATTTTAGTT
1 CTATTTACATTTT-GTT
1309108 CTATTTACATTTTGTT
1 CTATTTACATTTTGTT
*
1309124 TTATTT
1 CTATTT
1309130 TAATTTTGGC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 8 0.40
17 12 0.60
ACGTcount: A:0.21, C:0.08, G:0.05, T:0.67
Consensus pattern (16 bp):
CTATTTACATTTTGTT
Found at i:1309837 original size:131 final size:131
Alignment explanation
Indices: 1309604--1309958 Score: 507
Period size: 131 Copynumber: 2.7 Consensus size: 131
1309594 GAAAATAGTA
* * * *
1309604 ATATCTTTTCATTTCGGTTGGAGTAATAAATGATTG-TTTAA-GCATAAAAGGTCATTTATTCTC
1 ATATCTCTTCATTTCGATAGGAGTAATAAATGATTGCTTTAAGGCATAAGAGGTCATTTATTCTC
* * *
1309667 GATTGGAAATAATTAGATATTATCGTTTTCTCTCTAATCAATATTGATTTTTAAGACGGAAGAGT
66 GATTGGAAATAATTAGATATTATCGTTTTCTCTCGAATCAATATTGACTTTTAAGACGAAAGAGT
1309732 G
131 G
* * * * * *
1309733 ATATCTCTTCATTTCTATAGGAGTAACAAATGACTGCTTTAAGGCATGAGAGATCATTTATTCTT
1 ATATCTCTTCATTTCGATAGGAGTAATAAATGATTGCTTTAAGGCATAAGAGGTCATTTATTCTC
* * * *
1309798 GATTGGAAATCATTAGATATTATCATTTTCTCTCGAATCAATATTGACTTTTAAGATGAAATAGT
66 GATTGGAAATAATTAGATATTATCGTTTTCTCTCGAATCAATATTGACTTTTAAGACGAAAGAGT
1309863 G
131 G
** * *
1309864 ATATCTCTTTGTTTCGATCGGAGTAATAAATGATTGCTTTAAGACATAAGAGGTCATTTATTCTC
1 ATATCTCTTCATTTCGATAGGAGTAATAAATGATTGCTTTAAGGCATAAGAGGTCATTTATTCTC
1309929 GATTGGAAATAATTAGATATTATCGTTTTC
66 GATTGGAAATAATTAGATATTATCGTTTTC
1309959 GTTCTTAAAA
Statistics
Matches: 195, Mismatches: 29, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
129 30 0.15
130 5 0.03
131 160 0.82
ACGTcount: A:0.32, C:0.12, G:0.16, T:0.40
Consensus pattern (131 bp):
ATATCTCTTCATTTCGATAGGAGTAATAAATGATTGCTTTAAGGCATAAGAGGTCATTTATTCTC
GATTGGAAATAATTAGATATTATCGTTTTCTCTCGAATCAATATTGACTTTTAAGACGAAAGAGT
G
Found at i:1310558 original size:19 final size:19
Alignment explanation
Indices: 1310534--1310570 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
1310524 ATATTTATGT
1310534 TTTTTAAATAAA-AATATTA
1 TTTTTAAA-AAATAATATTA
1310553 TTTTTAAAAAATAATATT
1 TTTTTAAAAAATAATATT
1310571 TTAAAAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 3 0.18
19 14 0.82
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
TTTTTAAAAAATAATATTA
Found at i:1310564 original size:16 final size:15
Alignment explanation
Indices: 1310543--1310578 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
1310533 TTTTTTAAAT
*
1310543 AAAAATATTATTTTTA
1 AAAAATAATA-TTTTA
1310559 AAAAATAATATTTTA
1 AAAAATAATATTTTA
1310574 AAAAA
1 AAAAA
1310579 AAATCATCTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.53
16 9 0.47
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
AAAAATAATATTTTA
Found at i:1310579 original size:16 final size:16
Alignment explanation
Indices: 1310543--1310579 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
1310533 TTTTTTAAAT
* *
1310543 AAAAATATTATTTTTA
1 AAAAATAATATTTTAA
1310559 AAAAATAATATTTTAA
1 AAAAATAATATTTTAA
1310575 AAAAA
1 AAAAA
1310580 AATCATCTCA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
AAAAATAATATTTTAA
Found at i:1312854 original size:292 final size:293
Alignment explanation
Indices: 1312323--1312908 Score: 1003
Period size: 292 Copynumber: 2.0 Consensus size: 293
1312313 ACAGAACCTG
* *
1312323 CAGTTGAATATTGTTGAAGTCATATGGGAAATACCAATAATTAGAACTGTGCTACAGCTGTAAAT
1 CAGTTGAATATTGTTGAAGTCATAAGGGAAATACCAATAATTAGAACTGTGCTACAACTGTAAAT
* * *
1312388 CTTATCTCTTTTTAAGAATATACACAGGGCCTCCAACGTCTTAGCCTCGACCCTGGTAGAACCCT
66 CTTATCTCTTTTTAAGAATATACACAGGGCCTCCAACGTCTTAACCCCGACCCTGATAGAACCCT
* ** * *
1312453 AACATTATGTACGTTGACCTCGACCAGTTGTACTAGAACTTTAATTTTTTTAAACCATGAATCGA
131 AACATTATGTACATTGACCTCGACCAGTTGTACTAGAACCCTAATTTTTTAAAACCATGAATCAA
* * *
1312518 TTTTTTTATAAAAATTATTAGGGTAAACTAAATAAATGGTCACTTATGTTTAAGTGTCTCTTTTA
196 TTTTTTTATAAAAATTATTAGGGTAAACTAAATAAATAGTCACTTACGTTTAAGTGTCACTTTTA
1312583 TCCATTGATATTTAAAAACAAATAA-TTGATCA
261 TCCATTGATATTTAAAAACAAATAATTTGATCA
*
1312615 CAGTTGAATATTGTTGAAGTCATAAGGGAAATACCAATAATTAGAATTGTGCTACAACTGTAAAT
1 CAGTTGAATATTGTTGAAGTCATAAGGGAAATACCAATAATTAGAACTGTGCTACAACTGTAAAT
* *
1312680 CTTATCTTTTTTTAAGAATTTACACAGGGCCTCCAACGTCTTAACCCCGACCCTGATAGAACCCT
66 CTTATCTCTTTTTAAGAATATACACAGGGCCTCCAACGTCTTAACCCCGACCCTGATAGAACCCT
1312745 AACATTATGTACATTGACCTCGACCAGTTGTACTAGAACCCTAATTTTTTAAAACCATGAATCAA
131 AACATTATGTACATTGACCTCGACCAGTTGTACTAGAACCCTAATTTTTTAAAACCATGAATCAA
* *
1312810 TTTTTTTATAAAATTTATTAGGGTAAACTAAATAAATAGTCACTTACGTTTAAGTTTCACTTTTA
196 TTTTTTTATAAAAATTATTAGGGTAAACTAAATAAATAGTCACTTACGTTTAAGTGTCACTTTTA
1312875 TCCATTGATATTTAAAAACAAATAATTTGATCA
261 TCCATTGATATTTAAAAACAAATAATTTGATCA
1312908 C
1 C
1312909 TAAAGTTATC
Statistics
Matches: 275, Mismatches: 18, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
292 267 0.97
293 8 0.03
ACGTcount: A:0.35, C:0.17, G:0.13, T:0.35
Consensus pattern (293 bp):
CAGTTGAATATTGTTGAAGTCATAAGGGAAATACCAATAATTAGAACTGTGCTACAACTGTAAAT
CTTATCTCTTTTTAAGAATATACACAGGGCCTCCAACGTCTTAACCCCGACCCTGATAGAACCCT
AACATTATGTACATTGACCTCGACCAGTTGTACTAGAACCCTAATTTTTTAAAACCATGAATCAA
TTTTTTTATAAAAATTATTAGGGTAAACTAAATAAATAGTCACTTACGTTTAAGTGTCACTTTTA
TCCATTGATATTTAAAAACAAATAATTTGATCA
Found at i:1314783 original size:17 final size:17
Alignment explanation
Indices: 1314752--1314784 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1314742 TTTTTTATTA
1314752 TTAAATATAAAAATAAT
1 TTAAATATAAAAATAAT
1314769 TTAAA-ATAAATAATAA
1 TTAAATATAAA-AATAA
1314785 AATAATATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
TTAAATATAAAAATAAT
Found at i:1316036 original size:26 final size:26
Alignment explanation
Indices: 1316005--1316063 Score: 111
Period size: 25 Copynumber: 2.3 Consensus size: 26
1315995 GAGGAAAGGT
1316005 ATCAAAACAAGGCTATATATGAAAGC
1 ATCAAAACAAGGCTATATATGAAAGC
1316031 ATC-AAACAAGGCTATATATGAAAGC
1 ATCAAAACAAGGCTATATATGAAAGC
1316056 ATCAAAAC
1 ATCAAAAC
1316064 CAGGTTATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
25 25 0.78
26 7 0.22
ACGTcount: A:0.51, C:0.17, G:0.14, T:0.19
Consensus pattern (26 bp):
ATCAAAACAAGGCTATATATGAAAGC
Found at i:1323497 original size:32 final size:32
Alignment explanation
Indices: 1323456--1323529 Score: 148
Period size: 32 Copynumber: 2.3 Consensus size: 32
1323446 GTTGGATTTG
1323456 GTTCGAATTTAGTTAGAGTCTGATCAGATCTT
1 GTTCGAATTTAGTTAGAGTCTGATCAGATCTT
1323488 GTTCGAATTTAGTTAGAGTCTGATCAGATCTT
1 GTTCGAATTTAGTTAGAGTCTGATCAGATCTT
1323520 GTTCGAATTT
1 GTTCGAATTT
1323530 TGTTCGGGTC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 42 1.00
ACGTcount: A:0.24, C:0.12, G:0.22, T:0.42
Consensus pattern (32 bp):
GTTCGAATTTAGTTAGAGTCTGATCAGATCTT
Found at i:1327382 original size:25 final size:26
Alignment explanation
Indices: 1327342--1327392 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 26
1327332 ATCTCTATCA
**
1327342 CACAAGTAGCTATGTTATTCAAACTAT
1 CACAAGTA-CTATGTTAACCAAACTAT
1327369 CACAAGT-CTATGTTAACCAAACTA
1 CACAAGTACTATGTTAACCAAACTA
1327393 CTTATTCCCT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 15 0.68
27 7 0.32
ACGTcount: A:0.39, C:0.22, G:0.10, T:0.29
Consensus pattern (26 bp):
CACAAGTACTATGTTAACCAAACTAT
Found at i:1328366 original size:225 final size:225
Alignment explanation
Indices: 1327677--1328589 Score: 1335
Period size: 225 Copynumber: 4.0 Consensus size: 225
1327667 GAACAGAAAC
* * * **
1327677 AAATCCACATTTGACATAGTAATAAAAAATTGGAGTCAAGGAAAAGAAAACAAGTATTGGAATTA
1 AAATCCACATTTGACATAGCAAT-CAAAATCGGAGTCAAGGAAAAGAAAACAAGTATTGGAAAAA
* * *
1327742 TCCATGAACTTCAAATACCAGTGTAAGATGATACAAAGCATGCTAAAATGTGAGCTTATTAGATA
65 TCCATGCACTACAATTACCAGTGTAAGATGATACAAAGCATGCTAAAATGTGAGCTTATTAGA-A
* *
1327807 ATTCAAATGTTCAACAAAGTACCTCTC-ATCCTCAATTTTCGCCACATTTCATCTCTTCGAGCGC
129 CTTCAAATGTTCAACAAAGTACCTC-CGATCCTCAATTTTCGCCACATTTCATCTCTTCGAGCAC
* *
1327871 ACATTAAGCAAGAAATCCGTTATCACCGACTCA
193 ACATTAAGTAAGAAATCCGTTATCACCGACTCG
*
1327904 AAATCCACATTTGACATAGCAATCAAAATTGGAGTCAAGGAAAAGAAAACAAGTATTGGAAAAAT
1 AAATCCACATTTGACATAGCAATCAAAATCGGAGTCAAGGAAAAGAAAACAAGTATTGGAAAAAT
* * *
1327969 CCATGCACTACAATTACCAGTGTAAGATGAATTGATACAAAGCTTGCTAAAATGTTAGCTTCTTA
66 CCATGCACTACAATTACCAGTGT-A-A-G-A-TGATACAAAGCATGCTAAAATGTGAGCTTATTA
* * *
1328034 GTACTTCAAATGTTCAACAAAGTACCTACGATCCTCTATTTTCGCCACATTTCATCTCTTCGAGC
126 GAACTTCAAATGTTCAACAAAGTACCTCCGATCCTCAATTTTCGCCACATTTCATCTCTTCGAGC
* * *
1328099 GCACATTAAGTAACAAATCCGTTATCACCGACTAG
191 ACACATTAAGTAAGAAATCCGTTATCACCGACTCG
* *
1328134 AAATCCACATTTGACTTAGCAATCAAAATCGGAATCAAGGAAAAGAAAACAAGTATTGGAAAAAT
1 AAATCCACATTTGACATAGCAATCAAAATCGGAGTCAAGGAAAAGAAAACAAGTATTGGAAAAAT
*
1328199 CCATGCACTACAATTACCAGTGTAAGATGATACAAAGAATGCTAAAATGTGAGCTTATTAGAACT
66 CCATGCACTACAATTACCAGTGTAAGATGATACAAAGCATGCTAAAATGTGAGCTTATTAGAACT
* * * *
1328264 TCAAATGTTCAACAAAGTATCTCCAATCCTCAATTTTCACCACATTTTATCTCTTCGAGCACACA
131 TCAAATGTTCAACAAAGTACCTCCGATCCTCAATTTTCGCCACATTTCATCTCTTCGAGCACACA
* **
1328329 TTAAGTAAGAAATCTGTTATCAATGACTCG
196 TTAAGTAAGAAATCCGTTATCACCGACTCG
* * *
1328359 GAATCCACATTTGACATAGTAATCAAAATCGGAGTCAACGAAAAGAAAACAAGTATTGGAAAAAT
1 AAATCCACATTTGACATAGCAATCAAAATCGGAGTCAAGGAAAAGAAAACAAGTATTGGAAAAAT
* *
1328424 CCATGCATTACAATTACCA-TAGTAAGATGATACAAAGCATGCTAAAATGTTAGCTTATTAGAAC
66 CCATGCACTACAATTACCAGT-GTAAGATGATACAAAGCATGCTAAAATGTGAGCTTATTAGAAC
*
1328488 TTCAAATGTTCAACAAAGTACCTCCGATCCTCAATTTTTGCCACATTTCATCTCTTCGAGCACAC
130 TTCAAATGTTCAACAAAGTACCTCCGATCCTCAATTTTCGCCACATTTCATCTCTTCGAGCACAC
** * * * *
1328553 ATCGATTAAAAAATCTGTTATCACGGACTCG
195 ATTAAGTAAGAAATCCGTTATCACCGACTCG
1328584 AAATCC
1 AAATCC
1328590 GGCATTTTCG
Statistics
Matches: 621, Mismatches: 58, Indels: 16
0.89 0.08 0.02
Matches are distributed among these distances:
224 1 0.00
225 325 0.52
226 60 0.10
227 24 0.04
228 2 0.00
229 3 0.00
230 175 0.28
231 31 0.05
ACGTcount: A:0.39, C:0.20, G:0.14, T:0.27
Consensus pattern (225 bp):
AAATCCACATTTGACATAGCAATCAAAATCGGAGTCAAGGAAAAGAAAACAAGTATTGGAAAAAT
CCATGCACTACAATTACCAGTGTAAGATGATACAAAGCATGCTAAAATGTGAGCTTATTAGAACT
TCAAATGTTCAACAAAGTACCTCCGATCCTCAATTTTCGCCACATTTCATCTCTTCGAGCACACA
TTAAGTAAGAAATCCGTTATCACCGACTCG
Found at i:1332368 original size:77 final size:75
Alignment explanation
Indices: 1332244--1332397 Score: 265
Period size: 77 Copynumber: 2.0 Consensus size: 75
1332234 AAGAATGATG
*
1332244 AGCATCAATTACTTGTGCGCATGGGTAAGTGAAACTGCTGTAGTTTTTTTTCTTCTTTCAATCAA
1 AGCATCAATTACTTGTGCGCATGGCTAAGTGAAACTGCTGTAG--TTTTTT-TTCTTTCAATCAA
1332309 TTTCA-TTTTTAA
63 TTTCATTTTTTAA
1332321 AGCATCAATTACTTGTGCGCATGGCTAAGTGAAACTGCTGTAGTTTTTTTTCTTTCAATCAATTT
1 AGCATCAATTACTTGTGCGCATGGCTAAGTGAAACTGCTGTAGTTTTTTTTCTTTCAATCAATTT
1332386 CATTTTTTAA
66 CATTTTTTAA
1332396 AG
1 AG
1332398 AAACAAAGTT
Statistics
Matches: 75, Mismatches: 1, Indels: 4
0.94 0.01 0.05
Matches are distributed among these distances:
74 18 0.24
75 15 0.20
77 42 0.56
ACGTcount: A:0.25, C:0.16, G:0.16, T:0.44
Consensus pattern (75 bp):
AGCATCAATTACTTGTGCGCATGGCTAAGTGAAACTGCTGTAGTTTTTTTTCTTTCAATCAATTT
CATTTTTTAA
Found at i:1333664 original size:13 final size:13
Alignment explanation
Indices: 1333648--1333686 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
1333638 AAATAATAAA
*
1333648 AAAAAATTACAAT
1 AAAAAAGTACAAT
*
1333661 AAAAAAGTCCAAT
1 AAAAAAGTACAAT
1333674 AAAAAAGTA-AAT
1 AAAAAAGTACAAT
1333686 A
1 A
1333687 CAAATATAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
12 4 0.17
13 19 0.83
ACGTcount: A:0.69, C:0.08, G:0.05, T:0.18
Consensus pattern (13 bp):
AAAAAAGTACAAT
Found at i:1335748 original size:12 final size:12
Alignment explanation
Indices: 1335731--1335795 Score: 60
Period size: 12 Copynumber: 5.1 Consensus size: 12
1335721 CAAAAAATTA
1335731 ATTAAATAAAAT
1 ATTAAATAAAAT
1335743 ATTAAAATAATTAAAT
1 ATT-AAAT-A--AAAT
1335759 AATTAAATAAAAT
1 -ATTAAATAAAAT
*
1335772 ACT-AATAAAAT
1 ATTAAATAAAAT
*
1335783 ATTAAATATAAT
1 ATTAAATAAAAT
1335795 A
1 A
1335796 AAATGTACAT
Statistics
Matches: 44, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
11 10 0.23
12 13 0.30
13 8 0.18
14 1 0.02
15 1 0.02
16 8 0.18
17 3 0.07
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.34
Consensus pattern (12 bp):
ATTAAATAAAAT
Found at i:1335771 original size:29 final size:30
Alignment explanation
Indices: 1335729--1335790 Score: 92
Period size: 29 Copynumber: 2.1 Consensus size: 30
1335719 CACAAAAAAT
1335729 TAATTAAATAAAATA-T-TAAAATAATTAAA
1 TAATTAAATAAAATACTATAAAAT-ATTAAA
1335758 TAATTAAATAAAATACTAATAAAATATTAAA
1 TAATTAAATAAAATACT-ATAAAATATTAAA
1335789 TA
1 TA
1335791 TAATAAAATG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
29 15 0.50
30 1 0.03
31 8 0.27
32 6 0.20
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.34
Consensus pattern (30 bp):
TAATTAAATAAAATACTATAAAATATTAAA
Found at i:1338051 original size:6 final size:6
Alignment explanation
Indices: 1338040--1338067 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
1338030 AGCAACATGC
1338040 AAAAAT AAAAAT AAAAAT AAAAAT AAAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAA
1338068 GTCGGACTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (6 bp):
AAAAAT
Found at i:1338717 original size:9 final size:9
Alignment explanation
Indices: 1338703--1338734 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
1338693 AAATACAACC
1338703 TTTTTTCAT
1 TTTTTTCAT
1338712 TTTTTTCAT
1 TTTTTTCAT
1338721 TTTTTT-AT
1 TTTTTTCAT
1338729 TTTTTT
1 TTTTTT
1338735 AAAGTTAGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 8 0.35
9 15 0.65
ACGTcount: A:0.09, C:0.06, G:0.00, T:0.84
Consensus pattern (9 bp):
TTTTTTCAT
Found at i:1339573 original size:11 final size:12
Alignment explanation
Indices: 1339557--1339616 Score: 65
Period size: 12 Copynumber: 5.1 Consensus size: 12
1339547 GGGATCTGTA
1339557 AGAAATAA-AAT
1 AGAAATAATAAT
1339568 AGAAATAATAAT
1 AGAAATAATAAT
1339580 A-ATAATAATAAT
1 AGA-AATAATAAT
1339592 A-ATAATAATAAT
1 AGA-AATAATAAT
1339604 A-ATAATAATAAT
1 AGA-AATAATAAT
1339616 A
1 A
1339617 ATAAATGGGA
Statistics
Matches: 47, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
11 9 0.19
12 38 0.81
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.28
Consensus pattern (12 bp):
AGAAATAATAAT
Found at i:1339579 original size:3 final size:3
Alignment explanation
Indices: 1339571--1339620 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
1339561 ATAAAATAGA
1339571 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1339619 AA
1 AA
1339621 ATGGGACGAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1340229 original size:134 final size:134
Alignment explanation
Indices: 1339743--1340364 Score: 818
Period size: 134 Copynumber: 4.7 Consensus size: 134
1339733 GAAATCTTAT
* * * * * * *
1339743 GAGGGATTTGCTCCACTTCTTTTTGAGGGAAAATCAGATAT-GGGATCGTCGATTCATTCCACTA
1 GAGGGATATGTTCCGCTTCTTCTTGAGGGAAAATCAGATATGGGGA-AGTTGATTCATTCCACTG
* * * * *
1339807 TTATTCAGTGAAGATTGAATCGAGGTAGACTTGTTCCACTATTACTTAGGGAATATCAAATCTTG
65 TTACTCAGGGAAGATTGAATCGAGGCAGACTTGTTCCACTGTTACTCAGGGAATATCAAATCTTG
1339872 AAAGA
130 AAAGA
* * * *
1339877 GAGGGATTTGTTACGCTTCTTCCTGAGGGAAAATCAGATAT-GGGACGTTGATTCATTCCACTGT
1 GAGGGATATGTTCCGCTTCTTCTTGAGGGAAAATCAGATATGGGGAAGTTGATTCATTCCACTGT
* * * * *
1339941 TGCTCATGGAAGATTGAATCGAGGCAGACTTGTTCCATTGTTAATGAGGGAATATCAAATCTTGA
66 TACTCAGGGAAGATTGAATCGAGGCAGACTTGTTCCACTGTTACTCAGGGAATATCAAATCTTGA
1340006 AAGA
131 AAGA
* * * * *
1340010 GA-GGATATGTTCCGCTTCTTCTTTAAGGAAAATAAGATCTGAGGAAGTTGATTCATTCCACTGT
1 GAGGGATATGTTCCGCTTCTTCTTGAGGGAAAATCAGATATGGGGAAGTTGATTCATTCCACTGT
* * **
1340074 CACTCAGGTAAGATTGAATCGAGGTGGACTTGTTCCACTGTTACTCAGGGAATATCAAATCTTGA
66 TACTCAGGGAAGATTGAATCGAGGCAGACTTGTTCCACTGTTACTCAGGGAATATCAAATCTTGA
1340139 AAGA
131 AAGA
* * *
1340143 GAGGGATTTATTCTGCTTCTTCTTGAGGGAAAATCAGATATGGGGAAGTTGATTCATTCCACTGT
1 GAGGGATATGTTCCGCTTCTTCTTGAGGGAAAATCAGATATGGGGAAGTTGATTCATTCCACTGT
* * * *
1340208 CACTCAGGGATGATTGAATCGAGGCAGACTTGTTTCACTGTTACTCAGGGAATATCTAATCTTGA
66 TACTCAGGGAAGATTGAATCGAGGCAGACTTGTTCCACTGTTACTCAGGGAATATCAAATCTTGA
*
1340273 AAAA
131 AAGA
* ** * * *
1340277 TAAAGATATGTTCCGCTTCTTCTTGAGGTAAAATCAGATATGGGGAAGTTGATTCATTCAATTGT
1 GAGGGATATGTTCCGCTTCTTCTTGAGGGAAAATCAGATATGGGGAAGTTGATTCATTCCACTGT
1340342 TACTCAGGGAAGATTGAATCGAG
66 TACTCAGGGAAGATTGAATCGAG
1340365 TTCAATTCAT
Statistics
Matches: 426, Mismatches: 60, Indels: 4
0.87 0.12 0.01
Matches are distributed among these distances:
132 31 0.07
133 162 0.38
134 233 0.55
ACGTcount: A:0.29, C:0.15, G:0.23, T:0.32
Consensus pattern (134 bp):
GAGGGATATGTTCCGCTTCTTCTTGAGGGAAAATCAGATATGGGGAAGTTGATTCATTCCACTGT
TACTCAGGGAAGATTGAATCGAGGCAGACTTGTTCCACTGTTACTCAGGGAATATCAAATCTTGA
AAGA
Found at i:1340499 original size:14 final size:14
Alignment explanation
Indices: 1340480--1340520 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
1340470 GCAATTCATA
1340480 ATTTGGATTTGAAG
1 ATTTGGATTTGAAG
* *
1340494 ATTTGGATTTCACG
1 ATTTGGATTTGAAG
*
1340508 ATATGGATTTGAA
1 ATTTGGATTTGAA
1340521 AAACATTACC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.29, C:0.05, G:0.24, T:0.41
Consensus pattern (14 bp):
ATTTGGATTTGAAG
Found at i:1341376 original size:191 final size:191
Alignment explanation
Indices: 1340985--1341577 Score: 693
Period size: 190 Copynumber: 3.1 Consensus size: 191
1340975 GCCCGAGAGG
* * * * **
1340985 CTTACTGATGGCCCAAAAGACTTACCAAATTT-TAGAATAGTTTACTAGTTAAGAATTTTTTCTT
1 CTTACTGATGGCCCAAAGGACTTACCAACTTTGGA-AATAGTTTACTAGGTAAGAAACTTTTCTT
* * * * * * *
1341049 ACTTTTAAAAAAATTTCAATTTTCAGATTTAAGTAAAAAACTTTTCTCATTTTTTTTTGAA-AAA
65 ACTTTT-CAAAAATTTCAATTTTCAGATTTAAATGAGAAACCTTTCTCA---TTTTTTCAAGAGA
* * * * * *
1341113 CATGTGAAAACATCGTG-CTAGAATGTCTTATGGATGGCCCGAAGGACTTATCATCCTGCTCCAA
126 TATGTGAAAACATC-TGCCCA-AAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTTCTCGAA
*
1341177 TGA
189 AGA
*
1341180 CTTACTGATGGCCCAAAGGACTTACCAACTTTGGAAATAGTTTACTAGGTAAGAAACTTTCCTTA
1 CTTACTGATGGCCCAAAGGACTTACCAACTTTGGAAATAGTTTACTAGGTAAGAAACTTTTCTT-
* *
1341245 AC-TTTCAAAAATTTTAATTTTCATATTTAAATGAGAAACCTTTCTCA-TTTTTCAAGAGATATG
65 ACTTTTCAAAAATTTCAATTTTCAGATTTAAATGAGAAACCTTTCTCATTTTTTCAAGAGATATG
* *
1341308 TGAAAACATGCTGCCCAAAGGTCTTATGGATGGCCCGAAGAACTTATTATCTTTCTCGAAAGA
130 TGAAAACAT-CTGCCCAAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTTCTCGAAAGA
*
1341371 CTTACTGATTGCCC-AAGGACTTACCAACTTTGGAAATAGTTTACTAGGTAAGAAACTTTTCTTA
1 CTTACTGATGGCCCAAAGGACTTACCAACTTTGGAAATAGTTTACTAGGTAAGAAACTTTTCTTA
* *
1341435 CTTTTCAAAAATTTCAATTTGCAGATTTAAATGAGAAACCTTTC-CAGTTTTTTC-TGAGATATG
66 CTTTTCAAAAATTTCAATTTTCAGATTTAAATGAGAAACCTTTCTCA-TTTTTTCAAGAGATATG
* * * * *
1341498 TGAAAACATCCTGCTCGAAGGTCTTATGGATGGCTCGATGGAC-TATCATCTTGT-TTGAAAGA
130 TGAAAACAT-CTGCCCAAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTT-TCTCGAAAGA
* *
1341560 CTTACAGATGACCCAAAG
1 CTTACTGATGGCCCAAAG
1341578 AATTTAAGCA
Statistics
Matches: 346, Mismatches: 42, Indels: 25
0.84 0.10 0.06
Matches are distributed among these distances:
189 30 0.09
190 143 0.41
191 74 0.21
192 3 0.01
194 35 0.10
195 58 0.17
196 3 0.01
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Consensus pattern (191 bp):
CTTACTGATGGCCCAAAGGACTTACCAACTTTGGAAATAGTTTACTAGGTAAGAAACTTTTCTTA
CTTTTCAAAAATTTCAATTTTCAGATTTAAATGAGAAACCTTTCTCATTTTTTCAAGAGATATGT
GAAAACATCTGCCCAAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTTCTCGAAAGA
Found at i:1341848 original size:42 final size:41
Alignment explanation
Indices: 1341755--1341854 Score: 112
Period size: 42 Copynumber: 2.4 Consensus size: 41
1341745 GGTCTTATGG
* * *
1341755 ATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTTACAA
1 ATGGCACGAAGGACTTAACATCATGCTCGAAAGACTTACAA
* * *
1341796 ATGAG-ACGAAGGATTTAAACATCATGCTCTAAAGACTTACTA
1 ATG-GCACGAAGGACTT-AACATCATGCTCGAAAGACTTACAA
*
1341838 ATGGCTCGAAGGACTTA
1 ATGGCACGAAGGACTTA
1341855 CCAAGTTTGA
Statistics
Matches: 48, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
41 14 0.29
42 34 0.71
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.25
Consensus pattern (41 bp):
ATGGCACGAAGGACTTAACATCATGCTCGAAAGACTTACAA
Found at i:1341886 original size:229 final size:227
Alignment explanation
Indices: 1341362--1341936 Score: 798
Period size: 229 Copynumber: 2.5 Consensus size: 227
1341352 TATTATCTTT
* * * *
1341362 CTCGAAAGACTTACTGATTGCCCAAGGACTTACCAACTTTGGAAATAGTTTACTAGGTAAGAAAC
1 CTCGAAAGACTTACTAATGGCCGAAGGACTTACCAACTTTGAAAATAGTTTACTAGGTAAGAAAC
* * *
1341427 TTTTCTTACTTTTCAAAAATTTCAATTTGCAGATTTAAATGAGAAACCTTTCCAGTTTTTTCTGA
66 TTTTCTTACTTTTC-AAAATTTCAATTTTCAGATTTAAATGAGAAACC--TCCAG-TTTTCCAGA
* * * * *
1341492 GATATGTGAAAACATCCTGCTCGAAGGTCTTATGGATGGCTCGATGGACTATCATCTTGTTTGAA
127 GATATGTGAAAACATCCTGCCCGAAGGTCTTATGGATGGCCCGAAGGACTATCATCTTGCTCGAA
* * *
1341557 AGACTTACAGATGACCCAAAGAATTTAAGCATCATG
192 AGACTTACAAATGACACAAAGAATTTAAACATCATG
1341593 CTCGAAAGACTTA-TAGATGGCCCGAAGGACTTACCAACTTTGGAAAA-AGTTTACTAGGTAAGA
1 CTCGAAAGACTTACTA-ATGG-CCGAAGGACTTACCAACTTT-GAAAATAGTTTACTAGGTAAGA
*
1341656 AACTTTTCTTACTTTTCAAATATTTCAATTTTCATATTTAAATGAGAAACCT-CA-TTTTCCGAG
63 AACTTTTCTTACTTTTCAAA-ATTTCAATTTTCAGATTTAAATGAGAAACCTCCAGTTTTCC-AG
*
1341719 AGATATGTGAAAACATCCTGCCCTAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCG
126 AGATATGTGAAAACATCCTGCCCGAAGGTCTTATGGATGGCCCGAAGGAC-TATCATCTTGCTCG
* * *
1341784 AAAGACTTACAAATGAGACGAAGGATTTAAACATCATG
190 AAAGACTTACAAATGACACAAAGAATTTAAACATCATG
* * * *
1341822 CTCTAAAGACTTACTAATGGCTCGAAGGACTTACCAAGTTTGAAAATAGTTTAATAGATAAGAAA
1 CTCGAAAGACTTACTAATGGC-CGAAGGACTTACCAACTTTGAAAATAGTTTACTAGGTAAGAAA
1341887 CTTTTCTTACTTTTCACAAATTTCAATTTTCAGATTTAAATGAGAAACCT
65 CTTTTCTTACTTTTCA-AAATTTCAATTTTCAGATTTAAATGAGAAACCT
1341937 TTCTCATTTT
Statistics
Matches: 309, Mismatches: 25, Indels: 22
0.87 0.07 0.06
Matches are distributed among these distances:
227 5 0.02
228 53 0.17
229 142 0.46
230 6 0.02
231 19 0.06
232 80 0.26
233 4 0.01
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (227 bp):
CTCGAAAGACTTACTAATGGCCGAAGGACTTACCAACTTTGAAAATAGTTTACTAGGTAAGAAAC
TTTTCTTACTTTTCAAAATTTCAATTTTCAGATTTAAATGAGAAACCTCCAGTTTTCCAGAGATA
TGTGAAAACATCCTGCCCGAAGGTCTTATGGATGGCCCGAAGGACTATCATCTTGCTCGAAAGAC
TTACAAATGACACAAAGAATTTAAACATCATG
Found at i:1341954 original size:17 final size:17
Alignment explanation
Indices: 1341932--1341968 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
1341922 TTAAATGAGA
1341932 AACCTTTCTCATTTTTT
1 AACCTTTCTCATTTTTT
1341949 AACCTTTCTCATTTTTT
1 AACCTTTCTCATTTTTT
1341966 AAC
1 AAC
1341969 TTATAAAACG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.22, C:0.24, G:0.00, T:0.54
Consensus pattern (17 bp):
AACCTTTCTCATTTTTT
Found at i:1343738 original size:6 final size:6
Alignment explanation
Indices: 1343727--1343792 Score: 73
Period size: 6 Copynumber: 10.7 Consensus size: 6
1343717 TCTTTCTTTA
*
1343727 TTTTCT TTTTCT TTTTCT TTTTCC TTTTCTT TCTTTCTT TTTTCT TTTT-T
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTTC-T T-TTTC-T TTTTCT TTTTCT
1343777 TCTTT-T TTTTCT TTTT
1 T-TTTCT TTTTCT TTTT
1343793 TCGACTGTGG
Statistics
Matches: 54, Mismatches: 2, Indels: 8
0.84 0.03 0.12
Matches are distributed among these distances:
5 5 0.09
6 37 0.69
7 5 0.09
8 7 0.13
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (6 bp):
TTTTCT
Found at i:1343757 original size:37 final size:35
Alignment explanation
Indices: 1343715--1343783 Score: 68
Period size: 37 Copynumber: 1.9 Consensus size: 35
1343705 TTATTTATCA
* * *
1343715 TTTCTTTCTTTATTTTCTTTTTCTTTTTC-TTTTTCC
1 TTTCTTTCTTTATTTT-TTCTT-TTTTTCTTTTTCCT
*
1343751 TTTTCTTTCTTTCTTTTTTCTTTTTTTCTTTTT
1 TTT-CTTTCTTTATTTTTTCTTTTTTTCTTTTT
1343784 TTTCTTTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
35 6 0.21
36 11 0.38
37 12 0.41
ACGTcount: A:0.01, C:0.17, G:0.00, T:0.81
Consensus pattern (35 bp):
TTTCTTTCTTTATTTTTTCTTTTTTTCTTTTTCCT
Found at i:1343759 original size:28 final size:28
Alignment explanation
Indices: 1343728--1343793 Score: 89
Period size: 28 Copynumber: 2.4 Consensus size: 28
1343718 CTTTCTTTAT
1343728 TTTCTTTTTCTTTTTC-TTTTTCCTTTTC
1 TTTCTTTTT-TTTTTCTTTTTTCCTTTTC
* * *
1343756 TTTCTTTCTTTTTTCTTTTTTTCTTTTT
1 TTTCTTTTTTTTTTCTTTTTTCCTTTTC
1343784 TTTCTTTTTT
1 TTTCTTTTTT
1343794 CGACTGTGGT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
27 6 0.18
28 27 0.82
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (28 bp):
TTTCTTTTTTTTTTCTTTTTTCCTTTTC
Done.