Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002479.1 Hibiscus syriacus cultivar Beakdansim tig00005064_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: 87899
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:1084 original size:8 final size:8
Alignment explanation
Indices: 1041--1165 Score: 60
Period size: 8 Copynumber: 14.9 Consensus size: 8
1031 GAAAATGAAT
1041 AAAATAAA
1 AAAATAAA
*
1049 GAAAAGAAA
1 -AAAATAAA
1058 ATAAAGTAAA
1 A-AAA-TAAA
*
1068 GAAAT--A
1 AAAATAAA
1074 AAAATAAA
1 AAAATAAA
*
1082 AAAGTAATA
1 AAAATAA-A
1091 AAAAGTAAA
1 AAAA-TAAA
1100 TAAAATAATAA
1 -AAAAT-A-AA
1111 GAAAATAAA
1 -AAAATAAA
*
1120 GAAATAAA
1 AAAATAAA
* *
1128 GAAGTAAA
1 AAAATAAA
1136 AAAA-AAA
1 AAAATAAA
*
1143 ATAAA-GAA
1 A-AAATAAA
1151 AAAATAAA
1 AAAATAAA
*
1159 TAAATAA
1 AAAATAA
1166 GATAAAAAAG
Statistics
Matches: 91, Mismatches: 14, Indels: 23
0.71 0.11 0.18
Matches are distributed among these distances:
6 5 0.05
7 7 0.08
8 39 0.43
9 21 0.23
10 12 0.13
11 7 0.08
ACGTcount: A:0.77, C:0.00, G:0.09, T:0.14
Consensus pattern (8 bp):
AAAATAAA
Found at i:1092 original size:11 final size:11
Alignment explanation
Indices: 1076--1180 Score: 51
Period size: 11 Copynumber: 9.4 Consensus size: 11
1066 AAGAAATAAA
1076 AATAAAAAAGT
1 AATAAAAAAGT
1087 AAT-AAAAAGT
1 AATAAAAAAGT
1097 AAATAAAATAA-T
1 -AATAAAA-AAGT
* *
1109 AAGAAAATAAAGA
1 AA-TAAA-AAAGT
*
1122 AATAAAGAAGT
1 AATAAAAAAGT
*
1133 AA-AAAAAA-A
1 AATAAAAAAGT
*
1142 AATAAAGAAA-A
1 AATAAA-AAAGT
1153 AATAAATAAA-T
1 AATAAA-AAAGT
1164 AAGATAAAAAAGT
1 -A-ATAAAAAAGT
1177 AATA
1 AATA
1181 CAATAATGAC
Statistics
Matches: 74, Mismatches: 9, Indels: 22
0.70 0.09 0.21
Matches are distributed among these distances:
9 2 0.03
10 15 0.20
11 29 0.39
12 17 0.23
13 11 0.15
ACGTcount: A:0.75, C:0.00, G:0.09, T:0.16
Consensus pattern (11 bp):
AATAAAAAAGT
Found at i:1095 original size:10 final size:11
Alignment explanation
Indices: 1075--1162 Score: 54
Period size: 11 Copynumber: 7.6 Consensus size: 11
1065 AAAGAAATAA
1075 AAATAAAAAAGT
1 AAAT-AAAAAGT
1087 -AATAAAAAGT
1 AAATAAAAAGT
*
1097 AAATAAAATAAT
1 AAATAAAA-AGT
*
1109 AAGAAAATAAAG-
1 AA-ATAA-AAAGT
1121 AAATAAAGAAGT
1 AAATAAA-AAGT
* *
1133 AAAAAAAAAAAT
1 -AAATAAAAAGT
* *
1145 AAAGAAAAAAT
1 AAATAAAAAGT
1156 AAATAAA
1 AAATAAA
1163 TAAGATAAAA
Statistics
Matches: 61, Mismatches: 8, Indels: 15
0.73 0.10 0.18
Matches are distributed among these distances:
10 8 0.13
11 32 0.52
12 9 0.15
13 10 0.16
14 2 0.03
ACGTcount: A:0.77, C:0.00, G:0.08, T:0.15
Consensus pattern (11 bp):
AAATAAAAAGT
Found at i:1104 original size:60 final size:59
Alignment explanation
Indices: 1032--1162 Score: 151
Period size: 60 Copynumber: 2.2 Consensus size: 59
1022 AGGAAAAATG
* * *
1032 AAAATGAATAAAAT-A-AAGAAAAGAAAATAAAGTAAAGAAATAAAAATAAAAAAGT-AATAA
1 AAAATAAATAAAATAATAAGAAAA-AAAAGAAA-TAAAGAAATAAAAA-AAAAAA-TAAAGAA
* * *
1092 AAAGTAAATAAAATAATAAGAAAATAAAGAAATAAAGAAGTAAAAAAAAAAATAAAGAA
1 AAAATAAATAAAATAATAAGAAAAAAAAGAAATAAAGAAATAAAAAAAAAAATAAAGAA
1151 AAAATAAATAAA
1 AAAATAAATAAA
1163 TAAGATAAAA
Statistics
Matches: 61, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
58 1 0.02
59 21 0.34
60 25 0.41
61 7 0.11
62 7 0.11
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (59 bp):
AAAATAAATAAAATAATAAGAAAAAAAAGAAATAAAGAAATAAAAAAAAAAATAAAGAA
Found at i:1106 original size:16 final size:16
Alignment explanation
Indices: 1060--1178 Score: 61
Period size: 16 Copynumber: 7.4 Consensus size: 16
1050 AAAAGAAAAT
*
1060 AAAGTAAA-GAAATAA
1 AAAGTAAATAAAATAA
*
1075 AAA-TAAAAAAGTAATAA
1 AAAGTAAATAA--AATAA
1092 AAAGTAAATAAAATAA
1 AAAGTAAATAAAATAA
* *
1108 TAAGAAAATAAAGA-AA
1 AAAGTAAATAAA-ATAA
* *
1124 TAAAG-AAGTAAAAAAA
1 -AAAGTAAATAAAATAA
* *
1140 AAAATAAAGAAAA-AA
1 AAAGTAAATAAAATAA
*
1155 TAAA-TAAATAAGATAAA
1 -AAAGTAAATAAAAT-AA
1172 AAAGTAA
1 AAAGTAA
1179 TACAATAATG
Statistics
Matches: 81, Mismatches: 11, Indels: 22
0.71 0.10 0.19
Matches are distributed among these distances:
14 4 0.05
15 17 0.21
16 37 0.46
17 17 0.21
18 6 0.07
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (16 bp):
AAAGTAAATAAAATAA
Found at i:1129 original size:79 final size:78
Alignment explanation
Indices: 1042--1187 Score: 181
Period size: 80 Copynumber: 1.8 Consensus size: 78
1032 AAAATGAATA
* * *
1042 AAATAAAGAA-AAGAAAATAAAGTAAAGAAATAA-AAATAAAAAAG-TAATAAAAAGTAAATAAA
1 AAATAAAGAAGAA-AAAAAAAAATAAAGAAAAAATAAATAAAAAAGAT-A-AAAAAGT-AATAAA
1104 ATAATAAGAAAATAAAG
62 ATAATAAGAAAATAAAG
* *
1121 AAATAAAGAAGTAAAAAAAAAAATAAAGAAAAAATAAATAAATAAGATAAAAAAGTAATACAATA
1 AAATAAAGAAG-AAAAAAAAAAATAAAGAAAAAATAAATAAAAAAGATAAAAAAGTAATAAAATA
1186 AT
65 AT
1188 GACATCATAT
Statistics
Matches: 58, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
79 20 0.34
80 24 0.41
81 13 0.22
82 1 0.02
ACGTcount: A:0.75, C:0.01, G:0.09, T:0.16
Consensus pattern (78 bp):
AAATAAAGAAGAAAAAAAAAAATAAAGAAAAAATAAATAAAAAAGATAAAAAAGTAATAAAATAA
TAAGAAAATAAAG
Found at i:1133 original size:36 final size:34
Alignment explanation
Indices: 1032--1152 Score: 102
Period size: 36 Copynumber: 3.4 Consensus size: 34
1022 AGGAAAAATG
*
1032 AAAATGAATAAAATAAAGAAA-AGAAAA-TAAAGTAA
1 AAAAT-AAGAAAATAAAGAAATA-AAAAGTAAA-TAA
* * *
1067 AGAAATAAAAATAAAAAAGTAATAAAAAGTAAATAA
1 A-AAATAAGAA-AATAAAGAAATAAAAAGTAAATAA
*
1103 AATAATAAGAAAATAAAGAAATAAAGAAGTAAAAAAA
1 AA-AATAAGAAAATAAAGAAATAAA-AAGT-AAATAA
1140 AAAATAAAGAAAA
1 AAAAT-AAGAAAA
1153 AATAAATAAA
Statistics
Matches: 71, Mismatches: 7, Indels: 14
0.77 0.08 0.15
Matches are distributed among these distances:
35 18 0.25
36 34 0.48
37 19 0.27
ACGTcount: A:0.76, C:0.00, G:0.10, T:0.14
Consensus pattern (34 bp):
AAAATAAGAAAATAAAGAAATAAAAAGTAAATAA
Found at i:1142 original size:27 final size:26
Alignment explanation
Indices: 1042--1151 Score: 86
Period size: 27 Copynumber: 4.1 Consensus size: 26
1032 AAAATGAATA
*
1042 AAATAAAGAA-AAGAAAATAAAGTAAAG
1 AAATAAAGAATAA-AAAA-AAAATAAAG
1069 AAATAAA-AATAAAAAAGTAATAA-AAAG
1 AAATAAAGAATAAAAAA--AA-AATAAAG
* *
1096 TAAAT-AA-AATAATAAGAAAATAAAG
1 -AAATAAAGAATAAAAAAAAAATAAAG
1121 AAATAAAGAAGTAAAAAAAAAAATAAAG
1 AAATAAAGAA-T-AAAAAAAAAATAAAG
1149 AAA
1 AAA
1152 AAATAAATAA
Statistics
Matches: 69, Mismatches: 5, Indels: 17
0.76 0.05 0.19
Matches are distributed among these distances:
24 6 0.09
25 8 0.12
26 8 0.12
27 26 0.38
28 21 0.30
ACGTcount: A:0.76, C:0.00, G:0.10, T:0.14
Consensus pattern (26 bp):
AAATAAAGAATAAAAAAAAAATAAAG
Found at i:1162 original size:27 final size:28
Alignment explanation
Indices: 1042--1162 Score: 90
Period size: 28 Copynumber: 4.2 Consensus size: 28
1032 AAAATGAATA
1042 AAATAAAGAAAAGAAAATAAAGTAAAGAAAT
1 AAATAAA-AAAA-AAAATAAAG-AAAGAAAT
*
1073 AAA-AATAAAAAAGTAAT-AA-AAAGTAAAT
1 AAATAA-AAAAAA-AAATAAAGAAAG-AAAT
* * * *
1101 AAA-ATAATAAGAAAATAAAGAAATAAAG
1 AAATA-AAAAAAAAAATAAAGAAAGAAAT
*
1129 AAGTAAAAAAAAAAATAAAGAAA-AAAT
1 AAATAAAAAAAAAAATAAAGAAAGAAAT
1156 AAATAAA
1 AAATAAA
1163 TAAGATAAAA
Statistics
Matches: 72, Mismatches: 11, Indels: 18
0.71 0.11 0.18
Matches are distributed among these distances:
27 16 0.22
28 35 0.49
29 8 0.11
30 9 0.12
31 4 0.06
ACGTcount: A:0.77, C:0.00, G:0.09, T:0.14
Consensus pattern (28 bp):
AAATAAAAAAAAAAATAAAGAAAGAAAT
Found at i:1165 original size:19 final size:19
Alignment explanation
Indices: 1032--1165 Score: 89
Period size: 19 Copynumber: 6.8 Consensus size: 19
1022 AGGAAAAATG
*
1032 AAAATGAATAAAATAAAGAA
1 AAAATAAAT-AAATAAAGAA
*
1052 AAGA-AAATAAAGTAAAGAA
1 AAAATAAATAAA-TAAAGAA
*
1071 ATAA-AAATAAA-AAAGTAATA
1 AAAATAAATAAATAAAG--A-A
*
1091 AAAAGTAAATAAAATAATA-AG
1 AAAA-TAAAT-AAATAA-AGAA
*
1112 AAAATAAAGAAATAAAGAA
1 AAAATAAATAAATAAAGAA
*
1131 GTAAAA-AAAAAAATAAAGAA
1 --AAAATAAATAAATAAAGAA
1151 AAAATAAATAAATAA
1 AAAATAAATAAATAA
1166 GATAAAAAAG
Statistics
Matches: 91, Mismatches: 10, Indels: 27
0.71 0.08 0.21
Matches are distributed among these distances:
17 4 0.04
18 8 0.09
19 36 0.40
20 24 0.26
21 8 0.09
22 5 0.05
23 3 0.03
24 2 0.02
25 1 0.01
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (19 bp):
AAAATAAATAAATAAAGAA
Found at i:1233 original size:14 final size:15
Alignment explanation
Indices: 1214--1267 Score: 58
Period size: 14 Copynumber: 3.5 Consensus size: 15
1204 ATAATTCGGG
1214 ATAAAAAATAA-TAA
1 ATAAAAAATAAGTAA
*
1228 ATAAAAAA-AATTAA
1 ATAAAAAATAAGTAA
1242 ATTAAAAAATAAAAGTAA
1 A-TAAAAAAT--AAGTAA
1260 ATAAAAAA
1 ATAAAAAA
1268 ATGAATATAT
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
13 2 0.06
14 12 0.35
15 7 0.21
17 7 0.21
18 6 0.18
ACGTcount: A:0.78, C:0.00, G:0.02, T:0.20
Consensus pattern (15 bp):
ATAAAAAATAAGTAA
Found at i:1255 original size:18 final size:18
Alignment explanation
Indices: 1223--1269 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
1213 GATAAAAAAT
*
1223 AATAAATAAAA-AAAATTA
1 AATAAA-AAAATAAAAGTA
*
1241 AATTAAAAAATAAAAGTA
1 AATAAAAAAATAAAAGTA
1259 AATAAAAAAAT
1 AATAAAAAAAT
1270 GAATATATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 4 0.16
18 21 0.84
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.21
Consensus pattern (18 bp):
AATAAAAAAATAAAAGTA
Found at i:1334 original size:19 final size:20
Alignment explanation
Indices: 1298--1339 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
1288 TGTTAAGGAA
* *
1298 AAAAATATAGAATAATATAT
1 AAAAATAAAAAATAATATAT
1318 AAAAATAAAAAATATATATAT
1 AAAAATAAAAAATA-ATATAT
1339 A
1 A
1340 TAATAATAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (20 bp):
AAAAATAAAAAATAATATAT
Found at i:1493 original size:3 final size:3
Alignment explanation
Indices: 1473--1514 Score: 59
Period size: 3 Copynumber: 13.7 Consensus size: 3
1463 AAATAAGAAA
1473 AAT AATT AAT ATAT AAT AAT AAT AAT AAT AAT -AT AAT AAT AA
1 AAT AA-T AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1515 GGTTAAATTG
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
2 2 0.06
3 28 0.78
4 6 0.17
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
AAT
Found at i:1496 original size:20 final size:20
Alignment explanation
Indices: 1473--1514 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
1463 AAATAAGAAA
1473 AATAATTAAT-ATATAATAAT
1 AATAA-TAATAATATAATAAT
1493 AATAATAATAATATAATAAT
1 AATAATAATAATATAATAAT
1513 AA
1 AA
1515 GGTTAAATTG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (20 bp):
AATAATAATAATATAATAAT
Found at i:2396 original size:22 final size:21
Alignment explanation
Indices: 2366--2447 Score: 67
Period size: 22 Copynumber: 3.7 Consensus size: 21
2356 AAAAGTGAAA
2366 AAAATTAAATAAAATAGATAAG
1 AAAA-TAAATAAAATAGATAAG
* * *
2388 TAAAATAAAGAAAATAAAGAAG
1 -AAAATAAATAAAATAGATAAG
2410 AAAAATAAAT-AAATAAGATAAAG
1 -AAAATAAATAAAAT-AGAT-AAG
* *
2433 AAAGTAAATACAATA
1 AAAATAAATAAAATA
2448 ATGACAAAAT
Statistics
Matches: 47, Mismatches: 9, Indels: 7
0.75 0.14 0.11
Matches are distributed among these distances:
21 4 0.09
22 33 0.70
23 10 0.21
ACGTcount: A:0.71, C:0.01, G:0.10, T:0.18
Consensus pattern (21 bp):
AAAATAAATAAAATAGATAAG
Found at i:16275 original size:3 final size:3
Alignment explanation
Indices: 16255--16304 Score: 52
Period size: 3 Copynumber: 17.3 Consensus size: 3
16245 GGGCCCGCAA
* *
16255 AAT AAT ATAT AA- ATT AAT AAT AAT AAT AGT AAT AAT AAT -AT AAT
1 AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
16299 -AT AAT A
1 AAT AAT A
16305 TTTTTGTAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
2 5 0.13
3 31 0.79
4 3 0.08
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (3 bp):
AAT
Found at i:16275 original size:15 final size:16
Alignment explanation
Indices: 16255--16304 Score: 61
Period size: 15 Copynumber: 3.2 Consensus size: 16
16245 GGGCCCGCAA
*
16255 AATAATATATAA-ATT
1 AATAATATATAATAGT
16270 AATAATA-ATAATAGT
1 AATAATATATAATAGT
16285 AATAATAATATAATA-T
1 AATAAT-ATATAATAGT
16301 AATA
1 AATA
16305 TTTTTGTAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
14 4 0.13
15 15 0.48
16 6 0.19
17 6 0.19
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (16 bp):
AATAATATATAATAGT
Found at i:19401 original size:30 final size:30
Alignment explanation
Indices: 19367--19442 Score: 80
Period size: 31 Copynumber: 2.5 Consensus size: 30
19357 TTCATTTAAG
* * *
19367 TACCTAAAGTATTTTTTTAATTAAAATAAA
1 TACCTAAAGTATTTTTTCAATGAAAACAAA
* * *
19397 TACCTAAAGTTATCTTTTCGATGAAAACAGA
1 TACCTAAAG-TATTTTTTCAATGAAAACAAA
*
19428 CACCTAAAGTATTTT
1 TACCTAAAGTATTTT
19443 ATGTCAAAAT
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
30 14 0.38
31 23 0.62
ACGTcount: A:0.41, C:0.13, G:0.08, T:0.38
Consensus pattern (30 bp):
TACCTAAAGTATTTTTTCAATGAAAACAAA
Found at i:20496 original size:20 final size:20
Alignment explanation
Indices: 20471--20511 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
20461 CCATTAATTA
20471 AATATTTTATAAAAAATATT
1 AATATTTTATAAAAAATATT
* *
20491 AATATTTTTTATAAAATATT
1 AATATTTTATAAAAAATATT
20511 A
1 A
20512 TTTAAAATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
AATATTTTATAAAAAATATT
Found at i:20508 original size:14 final size:14
Alignment explanation
Indices: 20491--20540 Score: 57
Period size: 14 Copynumber: 3.4 Consensus size: 14
20481 AAAAAATATT
20491 AATATTTTTTATAA
1 AATATTTTTTATAA
*
20505 AATATTATTTA-AA
1 AATATTTTTTATAA
20518 ATATATTTTTTATTAAA
1 A-ATATTTTTTA-T-AA
20535 AATATT
1 AATATT
20541 AATTTCGTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
13 3 0.10
14 19 0.63
16 5 0.17
17 3 0.10
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (14 bp):
AATATTTTTTATAA
Found at i:29952 original size:22 final size:19
Alignment explanation
Indices: 29920--30038 Score: 72
Period size: 16 Copynumber: 6.3 Consensus size: 19
29910 GCAAAGAAAC
*
29920 TAAAAATATAATGAAAATAAA
1 TAAATATATAAT-AAAAT-AA
29941 TAAATAGTATAAATAAAATAA
1 TAAATA-TAT-AATAAAATAA
*
29962 TAAATATAT-AT-ATAT-A
1 TAAATATATAATAAAATAA
**
29978 TAAATATA-AA-AATGT-A
1 TAAATATATAATAAAATAA
**
29994 TGTATAATATAATAAAATAA
1 TAAAT-ATATAATAAAATAA
*
30014 TAAATA-GTAATAATAATAA
1 TAAATATATAATAA-AATAA
30033 TAAATA
1 TAAATA
30039 AATGAAAAAT
Statistics
Matches: 79, Mismatches: 10, Indels: 20
0.72 0.09 0.18
Matches are distributed among these distances:
16 17 0.22
17 6 0.08
18 10 0.13
19 15 0.19
20 7 0.09
21 13 0.16
22 8 0.10
23 3 0.04
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.32
Consensus pattern (19 bp):
TAAATATATAATAAAATAA
Found at i:30033 original size:19 final size:17
Alignment explanation
Indices: 29923--30055 Score: 87
Period size: 19 Copynumber: 7.4 Consensus size: 17
29913 AAGAAACTAA
29923 AAATATAATGAAAATAAAT
1 AAATATAAT-AAAAT-AAT
29942 AAATAGTATAAATAAAATAAT
1 -AA-A-TAT-AATAAAATAAT
*
29963 AAATAT-AT-ATATATAT
1 AAATATAATAAAATA-AT
* *
29979 AAATATAA-AAATGTATGT
1 AAATATAATAAA-ATA-AT
29997 ATAATATAATAAAATAAT
1 A-AATATAATAAAATAAT
30015 AAATAGTAATAATAATAAT
1 AAATA-TAATAA-AATAAT
*
30034 AAATA-AATGAAA-AAT
1 AAATATAATAAAATAAT
30049 AAATATA
1 AAATATA
30056 CATATAATAT
Statistics
Matches: 94, Mismatches: 7, Indels: 28
0.73 0.05 0.22
Matches are distributed among these distances:
15 12 0.13
16 13 0.14
17 10 0.11
18 16 0.17
19 21 0.22
20 7 0.07
21 4 0.04
22 8 0.09
23 3 0.03
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.31
Consensus pattern (17 bp):
AAATATAATAAAATAAT
Found at i:30689 original size:37 final size:37
Alignment explanation
Indices: 30648--30739 Score: 112
Period size: 37 Copynumber: 2.5 Consensus size: 37
30638 ATGTTTGTGG
* * *
30648 ATCCTATCTTTAGGAGTTTAAATAATAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTAAATAATAGCAAAACTCT
* ** *
30685 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATTCT
1 ATCCTATTTTTAGGAGTTTAAATAATAGCAAAACTCT
*
30722 ATCATATTTTTAGGAGTT
1 ATCCTATTTTTAGGAGTT
30740 CGAATCCTAA
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 47 1.00
ACGTcount: A:0.32, C:0.13, G:0.14, T:0.41
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTAAATAATAGCAAAACTCT
Found at i:31262 original size:106 final size:106
Alignment explanation
Indices: 31076--32244 Score: 1838
Period size: 106 Copynumber: 11.0 Consensus size: 106
31066 GCATTGTTCC
* * * *
31076 GAGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGGAATCGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
* * * *
31141 CCAGTC-GTCCATTCGTTGTGAAGTTGAACTTGTGTTGTCTC
66 CCAG-CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
31182 GAGTCCAATATCCTTTGTTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTATTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
*
31247 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTC
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
31288 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
*
31353 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTA
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* ** *
31394 GAGTCCAATATCCTTCGTTGTAAAGTTGAAATTGGCTCTGAAATTGATAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
31459 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
31500 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
* * *
31565 CCAGCGGTCCCTTCTTTGTGAAGTTGAACTTACGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
31606 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGATTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
31671 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
31712 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTAAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
31777 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
31818 GAATCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
*
31883 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
31924 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTAAAATTGGGAAATTATTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
31989 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
32030 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAATTGAGAAGTTGTTTGTTGAAAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
*
32095 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTTTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * ** * * *
32136 GAGTCCAATATCCTTCGCTATGAAGTTGAAATTGGCTCCAAAATTGGAAAATT-ATTGTTGTCAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
** * * *
32200 CCAGCCATCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
32241 GAGT
1 GAGT
32245 GACACGATAT
Statistics
Matches: 983, Mismatches: 79, Indels: 3
0.92 0.07 0.00
Matches are distributed among these distances:
105 48 0.05
106 935 0.95
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:32647 original size:18 final size:18
Alignment explanation
Indices: 32621--32656 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
32611 ATTGAATCCC
*
32621 CAAATAATGCCCCAATAT
1 CAAAAAATGCCCCAATAT
*
32639 CAAAAAATGCCCCCATAT
1 CAAAAAATGCCCCAATAT
32657 TTGATGTTGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.44, C:0.31, G:0.06, T:0.19
Consensus pattern (18 bp):
CAAAAAATGCCCCAATAT
Found at i:33095 original size:22 final size:22
Alignment explanation
Indices: 33069--33123 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
33059 TTGTGTTTGG
*
33069 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTAATGC
33091 TCAAAGGTTTGGCATTTAATGC
1 TCAAAGGTTTGGCATTTAATGC
33113 TCAAAGGTTTG
1 TCAAAGGTTTG
33124 ATGGGGTAGC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.25, C:0.13, G:0.25, T:0.36
Consensus pattern (22 bp):
TCAAAGGTTTGGCATTTAATGC
Found at i:33741 original size:16 final size:15
Alignment explanation
Indices: 33722--33793 Score: 56
Period size: 15 Copynumber: 4.5 Consensus size: 15
33712 TCCCTTTTTC
33722 TTTTTGATTTTTGTCTTT
1 TTTTTG-TTTTTGTC--T
33740 TTTTTGTTTTCT-TCT
1 TTTTTGTTTT-TGTCT
*
33755 TTTTTGTTTCTTTTCT
1 TTTTTGTTT-TTGTCT
* * *
33771 TTTTTATTTTTGGCC
1 TTTTTGTTTTTGTCT
33786 TTTTTGTT
1 TTTTTGTT
33794 CTGATTGAAT
Statistics
Matches: 46, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
15 21 0.46
16 12 0.26
17 6 0.13
18 7 0.15
ACGTcount: A:0.03, C:0.10, G:0.10, T:0.78
Consensus pattern (15 bp):
TTTTTGTTTTTGTCT
Found at i:33749 original size:17 final size:18
Alignment explanation
Indices: 33722--33782 Score: 54
Period size: 17 Copynumber: 3.3 Consensus size: 18
33712 TCCCTTTTTC
33722 TTTTTGATTTT-TGTCTTT
1 TTTTTGATTTTCT-TCTTT
33740 TTTTTG-TTTTCTTCTTT
1 TTTTTGATTTTCTTCTTT
** *
33757 TTTGTTTCTTTTCTTTTTT
1 TTT-TTGATTTTCTTCTTT
33776 ATTTTTG
1 -TTTTTG
33783 GCCTTTTTGT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
17 12 0.33
18 9 0.25
19 12 0.33
20 3 0.08
ACGTcount: A:0.03, C:0.08, G:0.08, T:0.80
Consensus pattern (18 bp):
TTTTTGATTTTCTTCTTT
Found at i:33752 original size:14 final size:14
Alignment explanation
Indices: 33717--33773 Score: 55
Period size: 14 Copynumber: 3.9 Consensus size: 14
33707 TTTTGTCCCT
33717 TTTTCTTTTTGATTT-
1 TTTTCTTTTT--TTTG
*
33732 TTGTCTTTTTTTTG
1 TTTTCTTTTTTTTG
33746 TTTTCTTCTTTTTTG
1 TTTTCTT-TTTTTTG
33761 -TTTCTTTTCTTTT
1 TTTTCTTTT-TTTT
33774 TTATTTTTGG
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
13 5 0.14
14 16 0.43
15 16 0.43
ACGTcount: A:0.02, C:0.11, G:0.07, T:0.81
Consensus pattern (14 bp):
TTTTCTTTTTTTTG
Found at i:37063 original size:19 final size:20
Alignment explanation
Indices: 37035--37072 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
37025 TGCAGATGAT
*
37035 GGAAATAAAAT-AAAAGAGA
1 GGAAAAAAAATGAAAAGAGA
37054 GGAAAAAAAATGAAAAGAG
1 GGAAAAAAAATGAAAAGAG
37073 TTAGTAAGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.68, C:0.00, G:0.24, T:0.08
Consensus pattern (20 bp):
GGAAAAAAAATGAAAAGAGA
Found at i:38375 original size:22 final size:21
Alignment explanation
Indices: 38328--38454 Score: 77
Period size: 22 Copynumber: 5.8 Consensus size: 21
38318 GCAAAGAAAC
38328 TAAAA-ATAT-AATGAAAATAA
1 TAAAATATATAAAT-AAAATAA
38348 -ATAAATAGTATAAATAAAATAA
1 TA-AAATA-TATAAATAAAATAA
38370 TAAAATATATATATATATATAA-ATA
1 TAAAATATATA-A-ATA-A-AATA-A
* ** *
38395 TAAAAATGTATGTATAATATAA
1 T-AAAATATATAAATAAAATAA
38417 TAAAATA-ATAAATAATAATAA
1 TAAAATATATAAATAA-AATAA
38438 TAATAATA-ATAAATAAA
1 TAA-AATATATAAATAAA
38455 TGAAAAATAA
Statistics
Matches: 85, Mismatches: 8, Indels: 27
0.71 0.07 0.22
Matches are distributed among these distances:
19 1 0.01
20 9 0.11
21 18 0.21
22 31 0.36
23 9 0.11
24 5 0.06
25 4 0.05
26 8 0.09
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.31
Consensus pattern (21 bp):
TAAAATATATAAATAAAATAA
Found at i:38397 original size:6 final size:6
Alignment explanation
Indices: 38356--38588 Score: 53
Period size: 6 Copynumber: 38.8 Consensus size: 6
38346 AAATAAATAG
* * * **
38356 TATAAA TA-AAA TAATAAAA TATATA TATATA TATAAA TATAAA AATGTA
1 TATAAA TATAAA T-AT-AAA TATAAA TATAAA TATAAA TATAAA TATAAA
*
38405 TGTATAA TAT-AA TA-AAA TAATAAA TA-ATAA TA-ATAA TAATAATA
1 TATA-AA TATAAA TATAAA T-ATAAA TATA-AA TATA-AA T-ATAA-A
* * * *
38449 AATAAA TGA-AAA -ATAAA TATACA TAT-AA TATTAA -CTAAA -A-AAA
1 TATAAA T-ATAAA TATAAA TATAAA TATAAA TATAAA TATAAA TATAAA
* * * *
38492 TAGTAATCA TAGAAA TATAAA -ATAAA -ATGAAG TA-AGAA TATATA TATATA
1 TA-TAA--A TATAAA TATAAA TATAAA TAT-AAA TATA-AA TATAAA TATAAA
* * * * * * *
38542 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATAA
1 TATAAA TATAAA TATAAA TATAAA TATAAA TATAAA TATAAA TATAA
38589 CGTTAGGAAA
Statistics
Matches: 180, Mismatches: 23, Indels: 48
0.72 0.09 0.19
Matches are distributed among these distances:
4 4 0.02
5 31 0.17
6 114 0.63
7 20 0.11
8 8 0.04
9 3 0.02
ACGTcount: A:0.61, C:0.01, G:0.03, T:0.35
Consensus pattern (6 bp):
TATAAA
Found at i:38426 original size:3 final size:3
Alignment explanation
Indices: 38408--38449 Score: 61
Period size: 3 Copynumber: 14.3 Consensus size: 3
38398 AAATGTATGT
38408 ATA AT- ATA ATA A-A ATA ATAA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA A
38450 ATAAATGAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
2 4 0.11
3 29 0.81
4 3 0.08
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:38467 original size:22 final size:21
Alignment explanation
Indices: 38415--38465 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 21
38405 TGTATAATAT
*
38415 AATAAAATAATAAATAATAAT
1 AATAAAATAATAAATAATAAA
38436 AATAATAATAATAAATAAATGAAA
1 AATAA-AATAATAAAT-AAT-AAA
38460 AATAAA
1 AATAAA
38466 TATACATATA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
21 5 0.19
22 10 0.38
23 4 0.15
24 7 0.27
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (21 bp):
AATAAAATAATAAATAATAAA
Found at i:38477 original size:30 final size:28
Alignment explanation
Indices: 38342--38478 Score: 83
Period size: 30 Copynumber: 4.8 Consensus size: 28
38332 AATATAATGA
*
38342 AAATAAATAA-ATAGTATAAATAAAATAAT
1 AAAT-AATAATATAATAT-AATAAAATAAT
38371 -AA-AAT-ATATATATATATATAAATATAA-
1 AAATAATAATATA-ATATA-ATAAA-ATAAT
* *
38398 AAAT-GTATGTATAATATAATAAAATAAT
1 AAATAATA-ATATAATATAATAAAATAAT
38426 AAATAATAATAATAATAATAAT-AAATAAAT
1 AAATAATAAT-ATAAT-ATAATAAAAT-AAT
38456 GAAA-AATAAATATACATATAATA
1 -AAATAAT-AATATA-ATATAATA
38479 TTAACTAAAA
Statistics
Matches: 86, Mismatches: 5, Indels: 32
0.70 0.04 0.26
Matches are distributed among these distances:
25 1 0.01
26 7 0.08
27 12 0.14
28 19 0.22
29 16 0.19
30 23 0.27
31 8 0.09
ACGTcount: A:0.65, C:0.01, G:0.03, T:0.31
Consensus pattern (28 bp):
AAATAATAATATAATATAATAAAATAAT
Found at i:38536 original size:2 final size:2
Alignment explanation
Indices: 38529--38587 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
38519 TGAAGTAAGA
38529 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
38571 AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT A
38588 ACGTTAGGAA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:38647 original size:2 final size:2
Alignment explanation
Indices: 38642--38683 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
38632 AGATAAAAAA
38642 AT AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
38683 A
1 A
38684 ATAGGAAAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:39907 original size:2 final size:2
Alignment explanation
Indices: 39900--39958 Score: 109
Period size: 2 Copynumber: 29.5 Consensus size: 2
39890 AGGAGAATGA
39900 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
*
39942 TC TC TC TC TC TG TC TC T
1 TC TC TC TC TC TC TC TC T
39959 GTGTGTGTGT
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.00, C:0.47, G:0.02, T:0.51
Consensus pattern (2 bp):
TC
Found at i:40332 original size:17 final size:17
Alignment explanation
Indices: 40310--40381 Score: 54
Period size: 17 Copynumber: 4.1 Consensus size: 17
40300 CTTTTAAGAC
*
40310 TTATTTTTATAAATAAA
1 TTATTTTTAAAAATAAA
* *
40327 TTATTTTTAAAAAGATA
1 TTATTTTTAAAAATAAA
**
40344 TTATATTAAAAAAATAAAA
1 TTAT-TTTTAAAAAT-AAA
* * *
40363 TTACTATTATAAATAAA
1 TTATTTTTAAAAATAAA
40380 TT
1 TT
40382 TTGAATTCTT
Statistics
Matches: 41, Mismatches: 12, Indels: 4
0.72 0.21 0.07
Matches are distributed among these distances:
17 23 0.56
18 13 0.32
19 5 0.12
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.44
Consensus pattern (17 bp):
TTATTTTTAAAAATAAA
Found at i:45225 original size:31 final size:31
Alignment explanation
Indices: 45190--45253 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
45180 ATATATGGTT
* *
45190 ACTTTCGTTTTTATTTAATTAAGGTATGATC
1 ACTTTCATTTTTATTTAATTAAGATATGATC
*
45221 ACTTTCATTTTTATTTAATTAAGATATGGTC
1 ACTTTCATTTTTATTTAATTAAGATATGATC
45252 AC
1 AC
45254 CATGGCTTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.28, C:0.11, G:0.11, T:0.50
Consensus pattern (31 bp):
ACTTTCATTTTTATTTAATTAAGATATGATC
Found at i:45903 original size:3 final size:3
Alignment explanation
Indices: 45895--45929 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
45885 CTCAATCTCA
45895 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
45930 AACCCAAATG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:46633 original size:23 final size:23
Alignment explanation
Indices: 46607--46651 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
46597 CACCACAGCT
*
46607 CGTATAATTGCACCGAAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCG
*
46630 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAATTGCACCGAAGTGCC
46652 ATATAATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.24, C:0.27, G:0.27, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCG
Found at i:46869 original size:149 final size:149
Alignment explanation
Indices: 46629--46933 Score: 556
Period size: 149 Copynumber: 2.0 Consensus size: 149
46619 CCGAAGTGCC
46629 GCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTATTCCTTAAGAA
1 GCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTATTCCTTAAGAA
*
46694 TCATATACATATACTAGGGATCAAGTATATGTCTTTCAAGACTTCACACATGTTCCACAGAATAT
66 TCATATACATATACTAGGGATCAAGTATATGTCTTTCAAGACTTCACACATGTTCCAAAGAATAT
* *
46759 ATATATATCCCGAAGGACT
131 ACATATATCCCGAAGGACA
46778 GCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTATTCCTTAAGAA
1 GCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTATTCCTTAAGAA
* *
46843 TCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCATACATGTTCCAAAGAATAT
66 TCATATACATATACTAGGGATCAAGTATATGTCTTTCAAGACTTCACACATGTTCCAAAGAATAT
*
46908 ACATATGTCCCGAAGGACA
131 ACATATATCCCGAAGGACA
46927 GCGTAGA
1 GCGTAGA
46934 CCCTCAACTC
Statistics
Matches: 150, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
149 150 1.00
ACGTcount: A:0.35, C:0.20, G:0.16, T:0.29
Consensus pattern (149 bp):
GCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTATTCCTTAAGAA
TCATATACATATACTAGGGATCAAGTATATGTCTTTCAAGACTTCACACATGTTCCAAAGAATAT
ACATATATCCCGAAGGACA
Found at i:48633 original size:21 final size:21
Alignment explanation
Indices: 48609--48653 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
48599 TTTTGTTCGT
* *
48609 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
48630 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
48651 TTG
1 TTG
48654 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:55495 original size:14 final size:14
Alignment explanation
Indices: 55473--55505 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
55463 TTTACTTCTT
*
55473 CCACTGTCGATCGA
1 CCACCGTCGATCGA
55487 CCACCGTCGATCGA
1 CCACCGTCGATCGA
55501 CCACC
1 CCACC
55506 ATCGGTCTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.21, C:0.45, G:0.18, T:0.15
Consensus pattern (14 bp):
CCACCGTCGATCGA
Found at i:55911 original size:23 final size:23
Alignment explanation
Indices: 55885--55937 Score: 56
Period size: 23 Copynumber: 2.3 Consensus size: 23
55875 AAAATATGTC
55885 TAAAAACGTTAA-ACTTTTTA-TAA
1 TAAAAAC-TTAATA-TTTTTATTAA
*
55908 TAAAAGACTTAATATTTTTATTAT
1 TAAAA-ACTTAATATTTTTATTAA
55932 TAAAAA
1 TAAAAA
55938 GACTTAACAC
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
23 16 0.62
24 10 0.38
ACGTcount: A:0.49, C:0.06, G:0.04, T:0.42
Consensus pattern (23 bp):
TAAAAACTTAATATTTTTATTAA
Found at i:57267 original size:14 final size:14
Alignment explanation
Indices: 57248--57274 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
57238 TGGGCATCCG
57248 AGGGCATCCGACCT
1 AGGGCATCCGACCT
57262 AGGGCATCCGACC
1 AGGGCATCCGACC
57275 GAGGCTATCC
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:0.22, C:0.37, G:0.30, T:0.11
Consensus pattern (14 bp):
AGGGCATCCGACCT
Found at i:57375 original size:29 final size:29
Alignment explanation
Indices: 57330--57434 Score: 129
Period size: 29 Copynumber: 3.6 Consensus size: 29
57320 GGAGCAGGAG
* * *
57330 GGAGTGCATGACAACCTATAAGGTCGCCA
1 GGAGTGCATGGCGACCTACAAGGTCGCCA
*
57359 GGAGTGCATGGCGACCTACAAGGTCGCCT
1 GGAGTGCATGGCGACCTACAAGGTCGCCA
** * *
57388 GGAAAGCATGGAGACCTACAAGGTCGCCC
1 GGAGTGCATGGCGACCTACAAGGTCGCCA
*
57417 GGAGGGCATGGCGACCTA
1 GGAGTGCATGGCGACCTA
57435 TGCTTGGGGA
Statistics
Matches: 65, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 65 1.00
ACGTcount: A:0.27, C:0.26, G:0.33, T:0.14
Consensus pattern (29 bp):
GGAGTGCATGGCGACCTACAAGGTCGCCA
Found at i:62939 original size:59 final size:59
Alignment explanation
Indices: 62822--62940 Score: 150
Period size: 59 Copynumber: 2.0 Consensus size: 59
62812 AGATATATGT
* * * **
62822 TTACACATACATGTGATATGTGACAGAAGAGAAGGAACATGTGATTATAAGATCAATGA
1 TTACACATACATGTGATACGTGACAGAAAAGAAAGAACATGTGATTATAAGAGAAATGA
* * *
62881 TTACACATACATGTGATACGTGACTGAAAAGAAA-AGATATGTGTTTATAAGAGAAATGA
1 TTACACATACATGTGATACGTGACAGAAAAGAAAGA-ACATGTGATTATAAGAGAAATGA
62940 T
1 T
62941 ATAATTAAGT
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
58 1 0.02
59 50 0.98
ACGTcount: A:0.43, C:0.09, G:0.21, T:0.27
Consensus pattern (59 bp):
TTACACATACATGTGATACGTGACAGAAAAGAAAGAACATGTGATTATAAGAGAAATGA
Found at i:63070 original size:31 final size:31
Alignment explanation
Indices: 63032--63187 Score: 206
Period size: 31 Copynumber: 5.0 Consensus size: 31
63022 AGGGTCGAGG
*
63032 GTTTACCTATGTTTTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
63063 GTTTACCTATGTTCTTCGGGACATATAGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
63094 GTTTACCTATGTTCTTCGGGATATATGAACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
63125 GTTTACCTATGTTATTCAGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * * *
63156 GATTACATAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
63187 G
1 G
63188 GTCCTTCGGG
Statistics
Matches: 109, Mismatches: 15, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
31 108 0.99
32 1 0.01
ACGTcount: A:0.23, C:0.17, G:0.21, T:0.39
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:63878 original size:14 final size:13
Alignment explanation
Indices: 63840--63878 Score: 53
Period size: 12 Copynumber: 3.0 Consensus size: 13
63830 GGTACTGTAG
63840 TAGGTATTGTTCA
1 TAGGTATTGTTCA
*
63853 TA-GTAATGTTCA
1 TAGGTATTGTTCA
63865 TACGGTATTGTTCA
1 TA-GGTATTGTTCA
63879 CTGTTCATAC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
12 11 0.50
13 2 0.09
14 9 0.41
ACGTcount: A:0.26, C:0.10, G:0.21, T:0.44
Consensus pattern (13 bp):
TAGGTATTGTTCA
Found at i:63902 original size:19 final size:21
Alignment explanation
Indices: 63859--63906 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
63849 TTCATAGTAA
**
63859 TGTTCATACGGTATTGTTCAC
1 TGTTCATACCATATTGTTCAC
63880 TGTTCATACCATATT-TT-AC
1 TGTTCATACCATATTGTTCAC
63899 TGTTCATA
1 TGTTCATA
63907 AAACGTATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 10 0.40
20 2 0.08
21 13 0.52
ACGTcount: A:0.23, C:0.19, G:0.12, T:0.46
Consensus pattern (21 bp):
TGTTCATACCATATTGTTCAC
Found at i:64425 original size:137 final size:137
Alignment explanation
Indices: 64077--65080 Score: 1277
Period size: 137 Copynumber: 7.4 Consensus size: 137
64067 GGTGTTACAC
* * *
64077 GCGCCTTCCCTTTTTTTATCAGAGAATATGTTATAATTGCACTATTATGTGTGATATCCCCC-GG
1 GCGCCTTCCCTTTTTTTGTCAGAGAATATGTTATAATTGCCCTATTATGTGTGATGTCCCCCGGG
* *
64141 GGCACTATTCATGTCAGTACCTATCATGTTTGAGGGGACACAACAAAGTGGTGAAAGAGCGTTTC
66 GGCACTATTCATGTCAGTACCTATCATGTTTGAGGGGACGCAACAAAGTGGTGAAAGCGCGTTTC
64206 AGGGGGA
131 AGGGGGA
* * * *
64213 GCACCTT-TCATTTTTTGTCAGAGAATATGTTTTAATTGCCCTATTATGTGTGATGTCCCCCGGG
1 GCGCCTTCCCTTTTTTTGTCAGAGAATATGTTATAATTGCCCTATTATGTGTGATGTCCCCCGGG
* * * * * * *
64277 GTCACTATTCATGCCAATACCTATCATGTTTGAGGGGACACAATAAAGTGGTGTAAGCGTGTTTC
66 GGCACTATTCATGTCAGTACCTATCATGTTTGAGGGGACGCAACAAAGTGGTGAAAGCGCGTTTC
64342 AGGGGGA
131 AGGGGGA
* * * *
64349 GTGCCTTCCCTTTTTTTCTCAGAGAATATGTTATAATTGTCATATTATGTGTGATGTCCCCCGGG
1 GCGCCTTCCCTTTTTTTGTCAGAGAATATGTTATAATTGCCCTATTATGTGTGATGTCCCCCGGG
* * * * *
64414 GGCACTATTCATATCAGTACCTATCATGTTTGAGGAGACGTATCAAAGTGGTGAAAGCACGTTTC
66 GGCACTATTCATGTCAGTACCTATCATGTTTGAGGGGACGCAACAAAGTGGTGAAAGCGCGTTTC
*
64479 AGGGGGC
131 AGGGGGA
* * * * * *
64486 GTGTCTT-ACATTTTTTGTTAGAGAATATGTTATAATTGCCCTATTATGTGTGATGTCCCCTGGG
1 GCGCCTTCCCTTTTTTTGTCAGAGAATATGTTATAATTGCCCTATTATGTGTGATGTCCCCCGGG
* * * * * *
64550 GGCACTATTTATGTCAGTACCTATCATGTTTAAGGGGACGCAAAAAAGTGGTGAAAACGTGTTTA
66 GGCACTATTCATGTCAGTACCTATCATGTTTGAGGGGACGCAACAAAGTGGTGAAAGCGCGTTTC
64615 AGGGGG-
131 AGGGGGA
*
64621 GCGCCTT-CCATTTTTTGTCAGAGAATATGTTATAATTGCCCTATTATGTGTGATGTCCCCCGGG
1 GCGCCTTCCCTTTTTTTGTCAGAGAATATGTTATAATTGCCCTATTATGTGTGATGTCCCCCGGG
* * *
64685 GGCACTAGTCATGTCAGTACCTATCATGTTTGAGGGGACGTAACAAAGTGGTGAAAGCGTGTTTC
66 GGCACTATTCATGTCAGTACCTATCATGTTTGAGGGGACGCAACAAAGTGGTGAAAGCGCGTTTC
64750 AGGGGGCA
131 AGGGGG-A
* * * * * * *
64758 -CGCCTTCCCTTTTTTTGTTAGAGATTACGTTATAAGTGCCCTATTATGTTTCATGTCCCCTGGG
1 GCGCCTTCCCTTTTTTTGTCAGAGAATATGTTATAATTGCCCTATTATGTGTGATGTCCCCCGGG
* * * *
64822 GGTACTATTCATATCAGTACCTATCATGTTTGAGGGGATGCAACAAAGTGGTGAAAGCGCATTTC
66 GGCACTATTCATGTCAGTACCTATCATGTTTGAGGGGACGCAACAAAGTGGTGAAAGCGCGTTTC
*
64887 AAGGGG-
131 AGGGGGA
* * * **
64893 GCACCTTCTCTTTTTTTTGTCAGAGAATATGTTATAATTGCCCTATTATGTGTGATGTCTCCTAG
1 GCGCCTTC-CCTTTTTTTGTCAGAGAATATGTTATAATTGCCCTATTATGTGTGATGTCCCCCGG
* * * * *
64958 GGGCACTATTCATGTCAGTACCTATCATGTTTGCGGGGACGCAATAATGTGGTGAAAACACGTTT
65 GGGCACTATTCATGTCAGTACCTATCATGTTTGAGGGGACGCAACAAAGTGGTGAAAGCGCGTTT
*
65023 CAGGGGGC
130 CAGGGGGA
* * * * * *
65031 GCACCTTTCTTTTTTTTTTCCA-ACTAATAGGTTATAATTGCCCTATTATG
1 GCGCCTTCCCTTTTTTTGT-CAGA-GAATATGTTATAATTGCCCTATTATG
65081 CTTGAAATTT
Statistics
Matches: 752, Mismatches: 106, Indels: 18
0.86 0.12 0.02
Matches are distributed among these distances:
135 171 0.23
136 200 0.27
137 348 0.46
138 33 0.04
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.34
Consensus pattern (137 bp):
GCGCCTTCCCTTTTTTTGTCAGAGAATATGTTATAATTGCCCTATTATGTGTGATGTCCCCCGGG
GGCACTATTCATGTCAGTACCTATCATGTTTGAGGGGACGCAACAAAGTGGTGAAAGCGCGTTTC
AGGGGGA
Found at i:64852 original size:408 final size:409
Alignment explanation
Indices: 64080--65080 Score: 1363
Period size: 408 Copynumber: 2.4 Consensus size: 409
64070 GTTACACGCG
* * * * *
64080 CCTTCCCT-TTTTTTATCAGAGAATATGTTATAATTGCACTATTATGTGTGATATCCCC-CGGGG
1 CCTTCTCTATTTTTTGTCAGAGAATATGTTATAATTGCCCTATTATGTGTGATGTCCCCTAGGGG
* *
64143 CACTATTCATGTCAGTACCTATCATGTTTGAGGGGACACAACAAAGTGGTGAAAGA-GCGTTTCA
66 CACTATTCATGTCAGTACCTATCATGTTTGAGGGGACGCAAAAAAGTGGTGAAA-ACGCGTTTCA
* *
64207 GGGGGAGCACCTTTCATTTTTTGTCAGAGAATATGTTTTAATTGCCCTATTATGTGTGATGTCCC
130 GGGGGAGCACCTTCCATTTTTTGTCAGAGAATATGTTATAATTGCCCTATTATGTGTGATGTCCC
* * * *
64272 CCGGGGTCACTATTCATGCCAATACCTATCATGTTTGAGGGGACACAATAAAGTGGTGTAAGCGT
195 CCGGGGGCACTAGTCATGCCAATACCTATCATGTTTGAGGGGACACAACAAAGTGGTGAAAGCGT
* * * * *
64337 GTTTCAGGGGGAGTGCCTTCCCTTTTTTTCTCAGAGAATATGTTATAATTGTCATATTATGTGTG
260 GTTTCAGGGGGAGCGCCTTCCCTTTTTTTCTCAGAGAATACGTTATAAGTGCCATATTATGTGTC
* *
64402 ATGTCCCCCGGGGGCACTATTCATATCAGTACCTATCATGTTTGAGGAGACGTATCAAAGTGGTG
325 ATGTCCCCCGGGGGCACTATTCATATCAGTACCTATCATGTTTGAGGAGACGCAACAAAGTGGTG
*
64467 AAAGCACGTTTC-AGGGGG-
390 AAAGCACATTTCAAGGGGGA
* * *
64485 CGTGTCT-TACATTTTTTGTTAGAGAATATGTTATAATTGCCCTATTATGTGTGATGTCCCCTGG
1 CCT-TCTCT--ATTTTTTGTCAGAGAATATGTTATAATTGCCCTATTATGTGTGATGTCCCCTAG
* * *
64549 GGGCACTATTTATGTCAGTACCTATCATGTTTAAGGGGACGCAAAAAAGTGGTGAAAACGTGTTT
63 GGGCACTATTCATGTCAGTACCTATCATGTTTGAGGGGACGCAAAAAAGTGGTGAAAACGCGTTT
* *
64614 AAGGGGG-GCGCCTTCCATTTTTTGTCAGAGAATATGTTATAATTGCCCTATTATGTGTGATGTC
128 CAGGGGGAGCACCTTCCATTTTTTGTCAGAGAATATGTTATAATTGCCCTATTATGTGTGATGTC
* * **
64678 CCCCGGGGGCACTAGTCATGTCAGTACCTATCATGTTTGAGGGGACGTAACAAAGTGGTGAAAGC
193 CCCCGGGGGCACTAGTCATGCCAATACCTATCATGTTTGAGGGGACACAACAAAGTGGTGAAAGC
* * * *
64743 GTGTTTCAGGGGGCA-CGCCTTCCCTTTTTTTGTTAGAGATTACGTTATAAGTGCCCTATTATGT
258 GTGTTTCAGGGGG-AGCGCCTTCCCTTTTTTTCTCAGAGAATACGTTATAAGTGCCATATTATGT
* * * * *
64807 TTCATGTCCCCTGGGGGTACTATTCATATCAGTACCTATCATGTTTGAGGGGATGCAACAAAGTG
322 GTCATGTCCCCCGGGGGCACTATTCATATCAGTACCTATCATGTTTGAGGAGACGCAACAAAGTG
*
64872 GTGAAAGCGCATTTCAAGGGGGCA
387 GTGAAAGCACATTTCAAGGGGG-A
* *
64896 CCTTCTCTTTTTTTTGTCAGAGAATATGTTATAATTGCCCTATTATGTGTGATGTCTCCTAGGGG
1 CCTTCTCTATTTTTTGTCAGAGAATATGTTATAATTGCCCTATTATGTGTGATGTCCCCTAGGGG
* * * *
64961 CACTATTCATGTCAGTACCTATCATGTTTGCGGGGACGCAATAATGTGGTGAAAACACGTTTCAG
66 CACTATTCATGTCAGTACCTATCATGTTTGAGGGGACGCAAAAAAGTGGTGAAAACGCGTTTCAG
* ** * * *
65026 GGGGCGCACCTTTCTTTTTTTTTTCCA-ACTAATAGGTTATAATTGCCCTATTATG
131 GGGGAGCACC-TTCCATTTTTTGT-CAGA-GAATATGTTATAATTGCCCTATTATG
65081 CTTGAAATTT
Statistics
Matches: 520, Mismatches: 61, Indels: 23
0.86 0.10 0.04
Matches are distributed among these distances:
405 3 0.01
406 2 0.00
408 282 0.54
409 186 0.36
410 7 0.01
411 14 0.03
412 26 0.05
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.34
Consensus pattern (409 bp):
CCTTCTCTATTTTTTGTCAGAGAATATGTTATAATTGCCCTATTATGTGTGATGTCCCCTAGGGG
CACTATTCATGTCAGTACCTATCATGTTTGAGGGGACGCAAAAAAGTGGTGAAAACGCGTTTCAG
GGGGAGCACCTTCCATTTTTTGTCAGAGAATATGTTATAATTGCCCTATTATGTGTGATGTCCCC
CGGGGGCACTAGTCATGCCAATACCTATCATGTTTGAGGGGACACAACAAAGTGGTGAAAGCGTG
TTTCAGGGGGAGCGCCTTCCCTTTTTTTCTCAGAGAATACGTTATAAGTGCCATATTATGTGTCA
TGTCCCCCGGGGGCACTATTCATATCAGTACCTATCATGTTTGAGGAGACGCAACAAAGTGGTGA
AAGCACATTTCAAGGGGGA
Found at i:65105 original size:20 final size:21
Alignment explanation
Indices: 65082--65128 Score: 73
Period size: 20 Copynumber: 2.4 Consensus size: 21
65072 CCTATTATGC
65082 TTGAAATTT-ATGTTAGAATG
1 TTGAAATTTGATGTTAGAATG
65102 TTG-AATTTGATGTTAGAATG
1 TTGAAATTTGATGTTAGAATG
65122 -TGAAATT
1 TTGAAATT
65129 GGGTTCTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 7 0.28
20 18 0.72
ACGTcount: A:0.34, C:0.00, G:0.21, T:0.45
Consensus pattern (21 bp):
TTGAAATTTGATGTTAGAATG
Found at i:66163 original size:42 final size:42
Alignment explanation
Indices: 66117--66206 Score: 119
Period size: 42 Copynumber: 2.1 Consensus size: 42
66107 GGCATGTAAC
**
66117 CTGGTGGGCTAGGAATATAACCC-TGCGGAGATGGTATATGAA
1 CTGGTGGGCTAGGAATAT-ACCCTTGCGGAGATGACATATGAA
* * *
66159 CTGGTGGGCTTGGCATATACCCTTGCGGAGATGACATCTGAA
1 CTGGTGGGCTAGGAATATACCCTTGCGGAGATGACATATGAA
66201 CTGGTG
1 CTGGTG
66207 TGCTGGACAT
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
41 4 0.10
42 38 0.90
ACGTcount: A:0.23, C:0.18, G:0.33, T:0.26
Consensus pattern (42 bp):
CTGGTGGGCTAGGAATATACCCTTGCGGAGATGACATATGAA
Found at i:66801 original size:17 final size:17
Alignment explanation
Indices: 66779--66814 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
66769 AAACTGAAAC
66779 ATAAATAT-ATAATTCTA
1 ATAAATATAAT-ATTCTA
66796 ATAAATATAATATTCTA
1 ATAAATATAATATTCTA
66813 AT
1 AT
66815 TATATCAAGC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 16 0.89
18 2 0.11
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.42
Consensus pattern (17 bp):
ATAAATATAATATTCTA
Found at i:67987 original size:25 final size:24
Alignment explanation
Indices: 67943--67989 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 24
67933 TAATTAGCAC
67943 AAATAATAATTAATTAATAAATTT
1 AAATAATAATTAATTAATAAATTT
67967 AAATAAATAA-TAATTATATAAAT
1 AAAT-AATAATTAATTA-ATAAAT
67990 ATTATTTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 10 0.48
25 11 0.52
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (24 bp):
AAATAATAATTAATTAATAAATTT
Found at i:68026 original size:14 final size:15
Alignment explanation
Indices: 68007--68041 Score: 56
Period size: 13 Copynumber: 2.5 Consensus size: 15
67997 TAATAAAAAA
68007 TAAAAAATTA-TTTT
1 TAAAAAATTATTTTT
68021 T-AAAAATTATTTTT
1 TAAAAAATTATTTTT
68035 TAAAAAA
1 TAAAAAA
68042 ATATAACAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 8 0.42
14 6 0.32
15 5 0.26
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (15 bp):
TAAAAAATTATTTTT
Found at i:68027 original size:13 final size:14
Alignment explanation
Indices: 68009--68040 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
67999 ATAAAAAATA
68009 AAAAATTA-TTTTT
1 AAAAATTATTTTTT
68022 AAAAATTATTTTTT
1 AAAAATTATTTTTT
68036 AAAAA
1 AAAAA
68041 AATATAACAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 8 0.44
14 10 0.56
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
AAAAATTATTTTTT
Found at i:72469 original size:9 final size:9
Alignment explanation
Indices: 72451--72485 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
72441 AGCTGCTCAG
*
72451 GACGACGAC
1 GACGATGAC
72460 GACGATGAC
1 GACGATGAC
*
72469 GACGATGAT
1 GACGATGAC
72478 GACGATGA
1 GACGATGA
72486 TGATGGTGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.34, C:0.20, G:0.34, T:0.11
Consensus pattern (9 bp):
GACGATGAC
Found at i:72486 original size:9 final size:9
Alignment explanation
Indices: 72460--72498 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
72450 GGACGACGAC
*
72460 GACGATGAC
1 GACGATGAT
72469 GACGATGAT
1 GACGATGAT
72478 GACGATGAT
1 GACGATGAT
* *
72487 GATGGTGAT
1 GACGATGAT
72496 GAC
1 GAC
72499 AGCGAGGAGT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.31, C:0.13, G:0.36, T:0.21
Consensus pattern (9 bp):
GACGATGAT
Found at i:72487 original size:12 final size:12
Alignment explanation
Indices: 72454--72490 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
72444 TGCTCAGGAC
*
72454 GACGACGACGAT
1 GACGACGATGAT
72466 GACGACGATGAT
1 GACGACGATGAT
*
72478 GACGATGATGAT
1 GACGACGATGAT
72490 G
1 G
72491 GTGATGACAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.32, C:0.16, G:0.35, T:0.16
Consensus pattern (12 bp):
GACGACGATGAT
Found at i:72794 original size:35 final size:33
Alignment explanation
Indices: 72755--72839 Score: 91
Period size: 35 Copynumber: 2.5 Consensus size: 33
72745 GTATTTTGTT
72755 TAATTTTGTT-TATTACCATTTAATATCAGTTATTG
1 TAATTTTGTTATATTACCATTTAATA-C--TTATTG
*
72790 TAATTTGGTTATCATTTACCATTTAATACTTATTG
1 TAATTTTGTTAT-A-TTACCATTTAATACTTATTG
* *
72825 TAAGTTTGTTGTATT
1 TAATTTTGTTATATT
72840 TAAAATTATA
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
33 2 0.05
34 1 0.02
35 24 0.56
36 1 0.02
37 2 0.05
38 13 0.30
ACGTcount: A:0.27, C:0.08, G:0.11, T:0.54
Consensus pattern (33 bp):
TAATTTTGTTATATTACCATTTAATACTTATTG
Found at i:77821 original size:24 final size:24
Alignment explanation
Indices: 77793--77839 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
77783 TTTTTATATA
*
77793 TAATAATATTACATATTTAATTAT
1 TAATAATATTACATATTAAATTAT
* *
77817 TAATAATTTTATATATTAAATTA
1 TAATAATATTACATATTAAATTA
77840 AACTAATAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (24 bp):
TAATAATATTACATATTAAATTAT
Found at i:79286 original size:221 final size:213
Alignment explanation
Indices: 78951--79381 Score: 623
Period size: 221 Copynumber: 2.0 Consensus size: 213
78941 TTTAAAATTA
* *
78951 TCAATATTAATATATTACGTATCAATATTTAAAATTTTGATTTTTTTTTGCGCAACCATATTTCT
1 TCAATAATAATATATTAAGTATCAATATTTAAAATTTTGATTTTTTTTTGCGCAACCATATTTCT
* *
79016 TATATATGAATAACATTTTCATCTTTCAACTTATTTTCTTACAATTTTTAAAAGTATCGATCATT
66 TATACATAAATAACATTTTCATCTTTCAACTTATTTTCTTACAATTTTTAAAAGTATCGATCATT
* *
79081 ACCACATAAGTATCGATATTTTAACTTTCGATCTTATCTTCAACTTTTTTTTAATAGTTAAAAAG
131 ACCACATAAGTATCGATATTTTAACTTTAGATCTTATCTTCAAC--TTTTTCAATA-TTAAAAAG
79146 TATCGATAATAATATATTAAG
193 TATCGATAATAATATATTAAG
* ** * *
79167 TCAATAATAATATATTAATTATTGATATTTAAAATTTTGATTTGTTTTTTTTTGCTCAACCGTAT
1 TCAATAATAATATATTAAGTATCAATATTTAAAATTTTGA----TTTTTTTTTGCGCAACCATAT
* *
79232 TT-TTAATACATAAATAACATTTTCAGTTTTTTAACTTATTTTCTTTA-AATTTTTAAAAGTATC
62 TTCTT-ATACATAAATAACATTTTCA-TCTTTCAACTTATTTTC-TTACAATTTTTAAAAGTATC
* *
79295 GATCATTACCGCATAAGTATCGATATTTTAACTTTAGATCTTATCTTCAACTTTTTCAATATTTA
124 GATCATTACCACATAAGTATCGATATTTTAACTTTAGATCTTATCTTCAACTTTTTCAATATTAA
79360 AAAGTATCGATAATAATATATT
189 AAAGTATCGATAATAATATATT
79382 CAGATCGATA
Statistics
Matches: 193, Mismatches: 15, Indels: 12
0.88 0.07 0.05
Matches are distributed among these distances:
216 35 0.18
218 25 0.13
219 11 0.06
220 39 0.20
221 80 0.41
222 3 0.02
ACGTcount: A:0.35, C:0.12, G:0.06, T:0.47
Consensus pattern (213 bp):
TCAATAATAATATATTAAGTATCAATATTTAAAATTTTGATTTTTTTTTGCGCAACCATATTTCT
TATACATAAATAACATTTTCATCTTTCAACTTATTTTCTTACAATTTTTAAAAGTATCGATCATT
ACCACATAAGTATCGATATTTTAACTTTAGATCTTATCTTCAACTTTTTCAATATTAAAAAGTAT
CGATAATAATATATTAAG
Found at i:79531 original size:40 final size:40
Alignment explanation
Indices: 79418--79531 Score: 103
Period size: 39 Copynumber: 2.9 Consensus size: 40
79408 GTTTTTTTTT
* *
79418 TGCGCAACCTATTTTATTAATAAAAATATTAACATAACTTA
1 TGCGCAACCTATTTTATTAAAAAAAATATTAACAT-TCTTA
** * *
79459 T-TACAACCTATTTCTATT--CAAAACTATT-ACATTC-TA
1 TGCGCAACCTATTT-TATTAAAAAAAATATTAACATTCTTA
*
79495 TGGCGCAACATATTTTATTAAAAAAAATATTAACATT
1 T-GCGCAACCTATTTTATTAAAAAAAATATTAACATT
79532 ACATTACAGA
Statistics
Matches: 57, Mismatches: 10, Indels: 13
0.71 0.12 0.16
Matches are distributed among these distances:
36 3 0.05
37 5 0.09
38 13 0.23
39 16 0.28
40 15 0.26
41 5 0.09
ACGTcount: A:0.42, C:0.16, G:0.04, T:0.38
Consensus pattern (40 bp):
TGCGCAACCTATTTTATTAAAAAAAATATTAACATTCTTA
Found at i:81493 original size:23 final size:23
Alignment explanation
Indices: 81434--81498 Score: 94
Period size: 23 Copynumber: 2.8 Consensus size: 23
81424 TGAATGATTA
*
81434 AGTGCTGACTGATTCAACAAAAC
1 AGTGCTGACTGATTCAGCAAAAC
* *
81457 AATGCTGACCGATTCAGCAAAAC
1 AGTGCTGACTGATTCAGCAAAAC
*
81480 AGTGCTGAATGATTCAGCA
1 AGTGCTGACTGATTCAGCA
81499 CAGAAGTACA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.37, C:0.22, G:0.20, T:0.22
Consensus pattern (23 bp):
AGTGCTGACTGATTCAGCAAAAC
Found at i:84616 original size:21 final size:21
Alignment explanation
Indices: 84592--84631 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
84582 CTGACTTGGA
*
84592 GATCCATGGTGCTGATGTGGC
1 GATCCAAGGTGCTGATGTGGC
* *
84613 GATCTAAGTTGCTGATGTG
1 GATCCAAGGTGCTGATGTG
84632 ACAGTTCACA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.17, C:0.15, G:0.35, T:0.33
Consensus pattern (21 bp):
GATCCAAGGTGCTGATGTGGC
Found at i:84734 original size:21 final size:21
Alignment explanation
Indices: 84708--84749 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
84698 TGACAGATTG
* *
84708 ACTGTCATGTCAATATCGTAA
1 ACTGTCACGTCAACATCGTAA
*
84729 ACTGTCACGTCAGCATCGTAA
1 ACTGTCACGTCAACATCGTAA
84750 TGGTCAAATG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.31, C:0.24, G:0.17, T:0.29
Consensus pattern (21 bp):
ACTGTCACGTCAACATCGTAA
Found at i:85589 original size:22 final size:23
Alignment explanation
Indices: 85540--85589 Score: 59
Period size: 22 Copynumber: 2.2 Consensus size: 23
85530 TGTGTTGCAC
85540 ATTTTCATATGCCTTTATGGCAT
1 ATTTTCATATGCCTTTATGGCAT
* *
85563 GTTTTCTTATG-CTTCT-TGGCAT
1 ATTTTCATATGCCTT-TATGGCAT
85585 ATTTT
1 ATTTT
85590 TCGGTTCTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
22 13 0.57
23 10 0.43
ACGTcount: A:0.16, C:0.16, G:0.14, T:0.54
Consensus pattern (23 bp):
ATTTTCATATGCCTTTATGGCAT
Found at i:86604 original size:18 final size:19
Alignment explanation
Indices: 86576--86621 Score: 67
Period size: 18 Copynumber: 2.4 Consensus size: 19
86566 ATTTTAAATT
86576 TAAATTATAAAAATTAAAAA
1 TAAA-TATAAAAATTAAAAA
*
86596 -AAATATAAATATTAAAAA
1 TAAATATAAAAATTAAAAA
86614 TAAATATA
1 TAAATATA
86622 TATTATTATT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 14 0.58
19 10 0.42
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (19 bp):
TAAATATAAAAATTAAAAA
Found at i:86624 original size:17 final size:17
Alignment explanation
Indices: 86588--86626 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
86578 AATTATAAAA
86588 ATTAAAAAAAATATAAAT
1 ATTAAAAAAAATAT-AAT
86606 ATTAAAAATAAATAT-AT
1 ATTAAAAA-AAATATAAT
86623 ATTA
1 ATTA
86627 TTATTTTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 6 0.30
18 8 0.40
19 6 0.30
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
ATTAAAAAAAATATAAT
Found at i:86817 original size:15 final size:16
Alignment explanation
Indices: 86794--86826 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
86784 AATTTCATAC
86794 ATAAATTTT-AATTTT
1 ATAAATTTTAAATTTT
*
86809 ATAACTTTTAAATTTT
1 ATAAATTTTAAATTTT
86825 AT
1 AT
86827 TTTTATATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (16 bp):
ATAAATTTTAAATTTT
Done.