Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006606.1 Hibiscus syriacus cultivar Beakdansim tig00016207_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: 88836
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:806 original size:14 final size:14
Alignment explanation
Indices: 787--832 Score: 57
Period size: 14 Copynumber: 3.6 Consensus size: 14
777 TTCAAGTCGT
787 AAATCATTACTATC
1 AAATCATTACTATC
801 AAATCATTAC--T-
1 AAATCATTACTATC
812 -AATCATTA-TATC
1 AAATCATTACTATC
824 AAATCATTA
1 AAATCATTA
833 AAGATTATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
10 8 0.29
11 1 0.04
12 1 0.04
13 8 0.29
14 10 0.36
ACGTcount: A:0.46, C:0.17, G:0.00, T:0.37
Consensus pattern (14 bp):
AAATCATTACTATC
Found at i:827 original size:23 final size:24
Alignment explanation
Indices: 788--877 Score: 93
Period size: 23 Copynumber: 3.9 Consensus size: 24
778 TCAAGTCGTA
788 AATCATTACTATCAAATCATTACT
1 AATCATTACTATCAAATCATTACT
812 AATCATTA-TATCAAATCATTA--
1 AATCATTACTATCAAATCATTACT
* **
833 AA-GATTA-TAAT-ATTTCATTACT
1 AATCATTACT-ATCAAATCATTACT
855 AAATCATTACTATCAAATCATTA
1 -AATCATTACTATCAAATCATTA
878 AAAAAATAAT
Statistics
Matches: 53, Mismatches: 6, Indels: 13
0.74 0.08 0.18
Matches are distributed among these distances:
20 12 0.23
21 4 0.08
23 15 0.28
24 14 0.26
25 8 0.15
ACGTcount: A:0.44, C:0.16, G:0.01, T:0.39
Consensus pattern (24 bp):
AATCATTACTATCAAATCATTACT
Found at i:927 original size:103 final size:104
Alignment explanation
Indices: 802--1088 Score: 355
Period size: 103 Copynumber: 2.8 Consensus size: 104
792 ATTACTATCA
802 AATCATTACT-AATCATT-ATATCAAATCATTAAAGATTATAATATTTCATTACTAAATCATTAC
1 AATCATTACTAAATCATTAATATCAAATCATTAAA-ATTATAATATTTCATTACTAAATCATTAC
* *
865 TATCAAATCATTAA-A-AAAATAATATTTTCATTATTACT
65 TATCAAATCATTAATATAAAATAACAATTTCATTATTACT
*
903 AATCATTACTAAATCATTAATATC-AA-CATTAAATATTAATAATATTATTATTACT-AATCATT
1 AATCATTACTAAATCATTAATATCAAATCATTAAA-ATT-ATAATATT-TCATTACTAAATCATT
**
965 ACTATC-AATCATTAATATTTAATAACAATTTCATTATTACT
63 ACTATCAAATCATTAATATAAAATAACAATTTCATTATTACT
*
1006 AATCATTACTAAATCATTAATATCAAATCATTAAAATTA-ATATAATTTCATTATTACTAATCAT
1 AATCATTACTAAATCATTAATATCAAATCATTAAAATTATA-AT-ATTTCATTACTA--AATCAT
*
1070 TA-T-T-AAATCATTATTATAA
62 TACTATCAAATCATTAATATAA
1089 TTTCATTACT
Statistics
Matches: 161, Mismatches: 11, Indels: 25
0.82 0.06 0.13
Matches are distributed among these distances:
101 29 0.18
102 32 0.20
103 64 0.40
104 20 0.12
105 8 0.05
106 8 0.05
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.42
Consensus pattern (104 bp):
AATCATTACTAAATCATTAATATCAAATCATTAAAATTATAATATTTCATTACTAAATCATTACT
ATCAAATCATTAATATAAAATAACAATTTCATTATTACT
Found at i:944 original size:58 final size:59
Alignment explanation
Indices: 847--982 Score: 176
Period size: 58 Copynumber: 2.4 Consensus size: 59
837 TTATAATATT
* * *
847 TCATTACTAAATCATTACTATCAAATCATTAAAA-AAATAATATTTTCATTATTACTAA
1 TCATTACTAAATCATTAATATCAAATCATTAAAATTAATAATAATTTCATTATTACTAA
905 TCATTACTAAATCATTAATATC-AA-CATTAAATATTAATAAT-A-TT-ATTATTACTAA
1 TCATTACTAAATCATTAATATCAAATCATTAAA-ATTAATAATAATTTCATTATTACTAA
960 TCATTACTATCAATCATTAATAT
1 TCATTACTA--AATCATTAATAT
983 TTAATAACAA
Statistics
Matches: 71, Mismatches: 3, Indels: 9
0.86 0.04 0.11
Matches are distributed among these distances:
55 20 0.28
56 9 0.13
57 15 0.21
58 27 0.38
ACGTcount: A:0.46, C:0.13, G:0.00, T:0.41
Consensus pattern (59 bp):
TCATTACTAAATCATTAATATCAAATCATTAAAATTAATAATAATTTCATTATTACTAA
Found at i:1009 original size:48 final size:46
Alignment explanation
Indices: 907--1028 Score: 155
Period size: 48 Copynumber: 2.7 Consensus size: 46
897 ATTACTAATC
* *
907 ATTACTAAATCATTAATATCAA-CATTAA-ATATTAATAATATTATT
1 ATTACT-AATCATTACTATCAATCATTAATATATTAATAAAATTATT
952 ATTACTAATCATTACTATCAATCATTAATAT-TTAATAACAATTTCATT
1 ATTACTAATCATTACTATCAATCATTAATATATTAATAA-AA-TT-ATT
1000 ATTACTAATCATTACTA--AATCATTAATAT
1 ATTACTAATCATTACTATCAATCATTAATAT
1029 CAAATCATTA
Statistics
Matches: 70, Mismatches: 2, Indels: 9
0.86 0.02 0.11
Matches are distributed among these distances:
44 14 0.20
45 19 0.27
46 15 0.21
47 2 0.03
48 20 0.29
ACGTcount: A:0.45, C:0.12, G:0.00, T:0.43
Consensus pattern (46 bp):
ATTACTAATCATTACTATCAATCATTAATATATTAATAAAATTATT
Found at i:1071 original size:13 final size:12
Alignment explanation
Indices: 1053--1089 Score: 58
Period size: 11 Copynumber: 3.1 Consensus size: 12
1043 TAATATAATT
1053 TCATTATTACTAA
1 TCATTATTA-TAA
1066 TCATTATTA-AA
1 TCATTATTATAA
1077 TCATTATTATAA
1 TCATTATTATAA
1089 T
1 T
1090 TTCATTACTA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 11 0.48
12 3 0.13
13 9 0.39
ACGTcount: A:0.41, C:0.11, G:0.00, T:0.49
Consensus pattern (12 bp):
TCATTATTATAA
Found at i:1080 original size:11 final size:11
Alignment explanation
Indices: 995--1085 Score: 53
Period size: 11 Copynumber: 7.8 Consensus size: 11
985 AATAACAATT
995 TCATTATTACTAA
1 TCATTATTA--AA
*
1008 TCATTACTAAA
1 TCATTATTAAA
1019 TCATTAATATCAAA
1 TCATT-AT-T-AAA
1033 TCATTA--AAA
1 TCATTATTAAA
* * *
1042 TTAATA-TAATT
1 TCATTATTAA-A
1053 TCATTATTACTAA
1 TCATTATTA--AA
1066 TCATTATTAAA
1 TCATTATTAAA
1077 TCATTATTA
1 TCATTATTA
1086 TAATTTCATT
Statistics
Matches: 62, Mismatches: 8, Indels: 18
0.70 0.09 0.20
Matches are distributed among these distances:
9 7 0.11
10 2 0.03
11 22 0.35
12 3 0.05
13 19 0.31
14 9 0.15
ACGTcount: A:0.44, C:0.12, G:0.00, T:0.44
Consensus pattern (11 bp):
TCATTATTAAA
Found at i:1175 original size:14 final size:14
Alignment explanation
Indices: 1156--1203 Score: 57
Period size: 14 Copynumber: 3.6 Consensus size: 14
1146 TTCAAGTCGT
1156 AAATCATTACTATC
1 AAATCATTACTATC
1170 AAATCATTAC--T-
1 AAATCATTACTATC
*
1181 AAATCATTAATATC
1 AAATCATTACTATC
*
1195 AAATTATTA
1 AAATCATTA
1204 AATATTAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
11 9 0.31
12 1 0.03
13 1 0.03
14 18 0.62
ACGTcount: A:0.48, C:0.15, G:0.00, T:0.38
Consensus pattern (14 bp):
AAATCATTACTATC
Found at i:1183 original size:25 final size:25
Alignment explanation
Indices: 1155--1203 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
1145 GTTCAAGTCG
*
1155 TAAATCATTACTATCAAATCATTAC
1 TAAATCATTAATATCAAATCATTAC
*
1180 TAAATCATTAATATCAAATTATTA
1 TAAATCATTAATATCAAATCATTA
1204 AATATTAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.47, C:0.14, G:0.00, T:0.39
Consensus pattern (25 bp):
TAAATCATTAATATCAAATCATTAC
Found at i:1212 original size:21 final size:22
Alignment explanation
Indices: 1175--1224 Score: 68
Period size: 21 Copynumber: 2.3 Consensus size: 22
1165 CTATCAAATC
*
1175 ATTACTAAATCATTAAT-ATCAA
1 ATTATTAAATCATTAATAAT-AA
1197 ATTATTAAAT-ATTAATAATAA
1 ATTATTAAATCATTAATAATAA
1218 ATTATTA
1 ATTATTA
1225 TTACTAATCA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 15 0.58
22 11 0.42
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (22 bp):
ATTATTAAATCATTAATAATAA
Found at i:1261 original size:47 final size:47
Alignment explanation
Indices: 1175--1296 Score: 160
Period size: 47 Copynumber: 2.6 Consensus size: 47
1165 CTATCAAATC
* * *
1175 ATTACTAAATCATTAATATCAAATTATTAAATATTAATAATAAATT-ATT
1 ATTACT-AATCATTACTATC-AATCATTAAAAATTAATAAT-AATTCATT
*
1224 ATTACTAATCATTACTATCAATCATTAAAAATTAATAATATTTCATT
1 ATTACTAATCATTACTATCAATCATTAAAAATTAATAATAATTCATT
1271 ATTACTAATCATTACTA--AATCATTAA
1 ATTACTAATCATTACTATCAATCATTAA
1297 TATCAAATCA
Statistics
Matches: 68, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
45 9 0.13
46 3 0.04
47 38 0.56
48 12 0.18
49 6 0.09
ACGTcount: A:0.48, C:0.11, G:0.00, T:0.42
Consensus pattern (47 bp):
ATTACTAATCATTACTATCAATCATTAAAAATTAATAATAATTCATT
Found at i:1307 original size:25 final size:25
Alignment explanation
Indices: 1277--1358 Score: 80
Period size: 25 Copynumber: 3.3 Consensus size: 25
1267 CATTATTACT
1277 AATCATTACTAAATCATTAATATCA
1 AATCATTACTAAATCATTAATATCA
* * **
1302 AATCATTA--AATATTAATAATAATTT
1 AATCATTACTAA-ATCATTAAT-ATCA
*
1327 AATCATTACT-AATCATTACTATCA
1 AATCATTACTAAATCATTAATATCA
1351 AATCATTA
1 AATCATTA
1359 AATATTAATA
Statistics
Matches: 44, Mismatches: 9, Indels: 9
0.71 0.15 0.15
Matches are distributed among these distances:
23 2 0.05
24 17 0.39
25 24 0.55
26 1 0.02
ACGTcount: A:0.48, C:0.13, G:0.00, T:0.39
Consensus pattern (25 bp):
AATCATTACTAAATCATTAATATCA
Found at i:1356 original size:49 final size:49
Alignment explanation
Indices: 1276--1396 Score: 188
Period size: 49 Copynumber: 2.4 Consensus size: 49
1266 TCATTATTAC
* *
1276 TAATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATT
1 TAATCATTACT-AATCATTACTATCAAATCATTAAATATTAATAACAATT
1326 TAATCATTACTAATCATTACTATCAAATCATTAAATATTAATAACAATT
1 TAATCATTACTAATCATTACTATCAAATCATTAAATATTAATAACAATT
* * *
1375 TCATTATCACTAATCATTACTA
1 TAATCATTACTAATCATTACTA
1397 AATCATTAAT
Statistics
Matches: 66, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
49 55 0.83
50 11 0.17
ACGTcount: A:0.46, C:0.14, G:0.00, T:0.40
Consensus pattern (49 bp):
TAATCATTACTAATCATTACTATCAAATCATTAAATATTAATAACAATT
Found at i:1408 original size:109 final size:106
Alignment explanation
Indices: 1171--1447 Score: 457
Period size: 109 Copynumber: 2.6 Consensus size: 106
1161 ATTACTATCA
* *
1171 AATCATTACTAAATCATTAATATCAAATTATTAAATATTAATAATAAATTATTATTACTAATCAT
1 AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTATTATTACTAATCAT
* *
1236 TACTATCAATCATTAAAAATTAATAATATTTCATTATTACT
66 TACTATCAATCATTAAAAATTAATAAAATTTCATTATCACT
*
1277 AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTAATCATTACTAATCA
1 AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTT-ATTATTACTAATCA
*
1342 TTACTATCAAATCATTAAATATTAATAACAATTTCATTATCACT
65 TTACTATC-AATCATTAAAAATTAATAA-AATTTCATTATCACT
1386 AATCATTACTAAATCATTAATATCAAATCATTAAATA-TAATAATAATTTCATTATTACTAAT
1 AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTT-ATTATTACTAAT
1448 TACTAAATAA
Statistics
Matches: 160, Mismatches: 8, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
106 48 0.30
107 21 0.13
108 41 0.26
109 50 0.31
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.41
Consensus pattern (106 bp):
AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTATTATTACTAATCAT
TACTATCAATCATTAAAAATTAATAAAATTTCATTATCACT
Found at i:1428 original size:59 final size:59
Alignment explanation
Indices: 1326--1447 Score: 201
Period size: 59 Copynumber: 2.1 Consensus size: 59
1316 AATAATAATT
*
1326 TAATCATTACTAATCATTACTATCAAATCATTAAATATTAATAACAATTTCATTATCAC
1 TAATCATTACTAATCATTAATATCAAATCATTAAATATTAATAACAATTTCATTATCAC
* *
1385 TAATCATTACTAAATCATTAATATCAAATCATTAAATA-TAATAATAATTTCATTATTAC
1 TAATCATTACT-AATCATTAATATCAAATCATTAAATATTAATAACAATTTCATTATCAC
1444 TAAT
1 TAAT
1448 TACTAAATAA
Statistics
Matches: 59, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
59 34 0.58
60 25 0.42
ACGTcount: A:0.46, C:0.14, G:0.00, T:0.40
Consensus pattern (59 bp):
TAATCATTACTAATCATTAATATCAAATCATTAAATATTAATAACAATTTCATTATCAC
Found at i:1536 original size:377 final size:374
Alignment explanation
Indices: 707--1673 Score: 1534
Period size: 377 Copynumber: 2.6 Consensus size: 374
697 TTTTAGTATC
*
707 AAATCATTATTATAATTTCATTACTAGTTATATAACGAAAATATGGTTAATTGAACCAAAC-TTG
1 AAATCATTATTATAATTTCATTACTAGTTATGTAACGAAAATATGGTTAATTGAACCAAACATTG
771 TT-ATTGTTCAAGTCGTAAATCATTACTATCAAATCATTACT-AATCATT-ATATCAAATCATTA
66 TTCATTGTTCAAGTCGTAAATCATTACTATCAAATCATTACTAAATCATTAATATCAAATCATTA
* *
833 AAGATT-ATAAT--ATT-TCATTACTAAATCATTACTATCAAATCATTAAAAA--AATAATATTT
131 AATATTAATAATAAATTATTATTACT-AATCATTACTATCAAATCATTAAAAATTAATAATA-TT
*
892 TCATTATTACTAATCATTACTAAATCATTAATATCAACATTAAATATTAATAATATTATTATTAC
194 TCATTATTACTAATCATTACTAAATCATTAATATCAACATTAAATATTAATAATATTATCATTAC
*
957 TAATCATTACTATCAATCATTAATATTTAATAACAATTTCATTATTACTAATCATTACTAAATCA
259 TAATCATTACTATCAATCATTAATATTTAATAACAATTTCATTATCACTAATCATTACTAAATCA
*
1022 TTAATATCAAATCATTAAAATTAATATAATTTCATTATTACTAATCATTATT
324 TTAATATCAAATCATTAAAATTAATATAATTTCATTATTACTAA-CATTACT
*
1074 AAATCATTATTATAATTTCATTACTAGTTTTGTAACGAAAATATGGTTAATTGAACCAAACATTG
1 AAATCATTATTATAATTTCATTACTAGTTATGTAACGAAAATATGGTTAATTGAACCAAACATTG
*
1139 TTCATTGTTCAAGTCGTAAATCATTACTATCAAATCATTACTAAATCATTAATATCAAATTATTA
66 TTCATTGTTCAAGTCGTAAATCATTACTATCAAATCATTACTAAATCATTAATATCAAATCATTA
1204 AATATTAATAATAAATTATTATTACTAATCATTACTATC-AATCATTAAAAATTAATAATATTTC
131 AATATTAATAATAAATTATTATTACTAATCATTACTATCAAATCATTAAAAATTAATAATATTTC
1268 ATTATTACTAATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTAATCAT
196 ATTATTACTAATCATTACTAAATCATTAATATC-AA-CATTAAATATTAATAAT-A-TT-ATCAT
1333 TACTAATCATTACTATCAAATCATTAA-ATATTAATAACAATTTCATTATCACTAATCATTACTA
256 TACTAATCATTACTATC-AATCATTAATAT-TTAATAACAATTTCATTATCACTAATCATTACTA
1397 AATCATTAATATCAAATCATT-AAATATAATAATAATTTCATTATTACT-A-ATTACT
319 AATCATTAATATCAAATCATTAAAAT-TAAT-ATAATTTCATTATTACTAACATTACT
*
1452 AAATAATTA-TATAATTTCATTACTAGTTATGTAACGAAAATATGGTTAATTGAACCAAACATTG
1 AAATCATTATTATAATTTCATTACTAGTTATGTAACGAAAATATGGTTAATTGAACCAAACATTG
1516 TTCATTGTTCAAGTCGTAAATCATTACTATCAAATCATTACTAAATCATTAATATCAAATCATTA
66 TTCATTGTTCAAGTCGTAAATCATTACTATCAAATCATTACTAAATCATTAATATCAAATCATTA
1581 AATATTAATAATAAATTATTATTATTAATCATTACTAATCATTACTATCAAATCATTAAAAATTA
131 AATATTAATAAT--A--A--ATTA-T--T-ATTACTAATCATTACTATCAAATCATTAAAAATTA
1646 ATAATAATTTCATTATTACTAATCATTA
186 ATAAT-ATTTCATTATTACTAATCATTA
1674 AATATTAAAT
Statistics
Matches: 558, Mismatches: 11, Indels: 40
0.92 0.02 0.07
Matches are distributed among these distances:
367 59 0.11
368 5 0.01
369 39 0.07
370 7 0.01
371 18 0.03
372 5 0.01
373 12 0.02
374 53 0.09
375 16 0.03
376 17 0.03
377 131 0.23
378 15 0.03
379 28 0.05
380 68 0.12
381 18 0.03
383 4 0.01
384 1 0.00
386 1 0.00
387 19 0.03
388 20 0.04
389 22 0.04
ACGTcount: A:0.44, C:0.12, G:0.03, T:0.41
Consensus pattern (374 bp):
AAATCATTATTATAATTTCATTACTAGTTATGTAACGAAAATATGGTTAATTGAACCAAACATTG
TTCATTGTTCAAGTCGTAAATCATTACTATCAAATCATTACTAAATCATTAATATCAAATCATTA
AATATTAATAATAAATTATTATTACTAATCATTACTATCAAATCATTAAAAATTAATAATATTTC
ATTATTACTAATCATTACTAAATCATTAATATCAACATTAAATATTAATAATATTATCATTACTA
ATCATTACTATCAATCATTAATATTTAATAACAATTTCATTATCACTAATCATTACTAAATCATT
AATATCAAATCATTAAAATTAATATAATTTCATTATTACTAACATTACT
Found at i:1552 original size:14 final size:14
Alignment explanation
Indices: 1533--1580 Score: 66
Period size: 14 Copynumber: 3.6 Consensus size: 14
1523 TTCAAGTCGT
1533 AAATCATTACTATC
1 AAATCATTACTATC
1547 AAATCATTAC--T-
1 AAATCATTACTATC
*
1558 AAATCATTAATATC
1 AAATCATTACTATC
1572 AAATCATTA
1 AAATCATTA
1581 AATATTAATA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
11 9 0.30
12 1 0.03
13 1 0.03
14 19 0.63
ACGTcount: A:0.48, C:0.17, G:0.00, T:0.35
Consensus pattern (14 bp):
AAATCATTACTATC
Found at i:1560 original size:25 final size:25
Alignment explanation
Indices: 1532--1580 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
1522 GTTCAAGTCG
*
1532 TAAATCATTACTATCAAATCATTAC
1 TAAATCATTAATATCAAATCATTAC
1557 TAAATCATTAATATCAAATCATTA
1 TAAATCATTAATATCAAATCATTA
1581 AATATTAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.47, C:0.16, G:0.00, T:0.37
Consensus pattern (25 bp):
TAAATCATTAATATCAAATCATTAC
Found at i:1596 original size:21 final size:21
Alignment explanation
Indices: 1532--1590 Score: 64
Period size: 25 Copynumber: 2.6 Consensus size: 21
1522 GTTCAAGTCG
*
1532 TAAATCATTACTATCAAATCATT
1 TAAAT-ATTAATATCAAATCA-T
1555 ACTAAATCATTAATATCAAATCAT
1 --TAAAT-ATTAATATCAAATCAT
1579 TAAATATTAATA
1 TAAATATTAATA
1591 ATAAATTATT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
21 7 0.21
22 5 0.15
24 1 0.03
25 20 0.61
ACGTcount: A:0.49, C:0.14, G:0.00, T:0.37
Consensus pattern (21 bp):
TAAATATTAATATCAAATCAT
Found at i:1623 original size:58 final size:60
Alignment explanation
Indices: 1548--1673 Score: 202
Period size: 58 Copynumber: 2.1 Consensus size: 60
1538 ATTACTATCA
* *
1548 AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAAATT-ATTATTATT
1 AATCATTACTAAATCATTAATATCAAATCATTAAAAATTAATAATAAATTCATTATTACT
* *
1607 AATCATTACT-AATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACT
1 AATCATTACTAAATCATTAATATCAAATCATTAAAAATTAATAATAAATTCATTATTACT
1666 AATCATTA
1 AATCATTA
1674 AATATTAAAT
Statistics
Matches: 62, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
58 36 0.58
59 26 0.42
ACGTcount: A:0.48, C:0.11, G:0.00, T:0.41
Consensus pattern (60 bp):
AATCATTACTAAATCATTAATATCAAATCATTAAAAATTAATAATAAATTCATTATTACT
Found at i:1682 original size:7 final size:8
Alignment explanation
Indices: 1666--1727 Score: 51
Period size: 7 Copynumber: 7.9 Consensus size: 8
1656 CATTATTACT
1666 AATCATTA
1 AATCATTA
1674 AAT-ATTA
1 AATCATTA
1681 AATCATTACTA
1 AATCA-T--TA
1692 AATCATT-
1 AATCATTA
*
1699 AAT-ATCA
1 AATCATTA
1706 AATCATTA
1 AATCATTA
*
1714 AAT-ATCA
1 AATCATTA
1721 AATCATT
1 AATCATT
1728 GTTCAAGTAG
Statistics
Matches: 43, Mismatches: 4, Indels: 14
0.70 0.07 0.23
Matches are distributed among these distances:
6 2 0.05
7 19 0.44
8 13 0.30
9 1 0.02
10 1 0.02
11 7 0.16
ACGTcount: A:0.50, C:0.13, G:0.00, T:0.37
Consensus pattern (8 bp):
AATCATTA
Found at i:1702 original size:25 final size:25
Alignment explanation
Indices: 1607--1786 Score: 124
Period size: 25 Copynumber: 7.3 Consensus size: 25
1597 TATTATTATT
*
1607 AATCATTACT-AATCATTACTATCA
1 AATCATTACTAAATCATTAATATCA
* * * **
1631 AATCATTA-AAAATTAATAATAATTT
1 AATCATTACTAAATCATTAAT-ATCA
* * *
1656 CATTATTACT-AATCATTAAATATTA
1 AATCATTACTAAATCATT-AATATCA
1681 AATCATTACTAAATCATTAATATCA
1 AATCATTACTAAATCATTAATATCA
*
1706 AATCATTA--AATATCA--AATCAT-T
1 AATCATTACTAA-ATCATTAAT-ATCA
** * * *
1728 GTTCAAGTAGTAAATCATTACTATCA
1 AATC-ATTACTAAATCATTAATATCA
1754 AATCATTACTAAATCATTAATATCA
1 AATCATTACTAAATCATTAATATCA
1779 AATCATTA
1 AATCATTA
1787 AATATTAATA
Statistics
Matches: 117, Mismatches: 26, Indels: 25
0.70 0.15 0.15
Matches are distributed among these distances:
22 5 0.04
23 7 0.06
24 23 0.20
25 68 0.58
26 14 0.12
ACGTcount: A:0.47, C:0.14, G:0.02, T:0.38
Consensus pattern (25 bp):
AATCATTACTAAATCATTAATATCA
Found at i:1704 original size:133 final size:134
Alignment explanation
Indices: 1534--1885 Score: 352
Period size: 133 Copynumber: 2.6 Consensus size: 134
1524 TCAAGTCGTA
* *
1534 AATCATTACTATCAAATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAAATTA
1 AATCATTAATATTAAATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAAATTA
* *
1599 TTATTATTAATCATTACTAATCATTACTATCAAATCATTA-AAA-ATTAATA-ATAAT-TTCATT
66 TTATTA-TAATCATTACTAATCATTACTATCAAATCATTACAAACATTAATATA-AATATTAAAT
*
1660 ATTACT
129 ATTAAT
* *
1666 AATCATTAAATATTAAATCATTACTAAATCATTAATATCAAATCATTAAATA-TCA-AAT-CATT
1 AATCATT-AATATTAAATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAAATT
* * * *
1728 -GT-TCA-AGT-AGTA--AATCATTACTATCAAATCATTACTAAATCATTAATATCAAATCATTA
65 ATTATTATAATCATTACTAATCATTACTATCAAATCATTAC-AAA-CATTAATAT-AAAT-ATTA
1787 AATATTAAT
126 AATATTAAT
* * *
1796 AATAATTTCATTATTACTAATCATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAA
1 AATCA-TT-AATATTA--AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAA
* *
1861 TTTCATCATTACTAATCATTACTAA
62 ATT-ATTATTA-TAATCATTACTAA
1886 ATCTTATAAA
Statistics
Matches: 174, Mismatches: 23, Indels: 34
0.75 0.10 0.15
Matches are distributed among these distances:
123 22 0.13
125 6 0.03
126 2 0.01
127 7 0.04
128 5 0.03
129 2 0.01
130 16 0.09
131 11 0.06
132 9 0.05
133 78 0.45
134 2 0.01
135 3 0.02
136 2 0.01
139 2 0.01
141 2 0.01
142 3 0.02
144 2 0.01
ACGTcount: A:0.47, C:0.13, G:0.01, T:0.39
Consensus pattern (134 bp):
AATCATTAATATTAAATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAAATTA
TTATTATAATCATTACTAATCATTACTATCAAATCATTACAAACATTAATATAAATATTAAATAT
TAAT
Found at i:1710 original size:14 final size:14
Alignment explanation
Indices: 1666--1787 Score: 87
Period size: 14 Copynumber: 8.6 Consensus size: 14
1656 CATTATTACT
*
1666 AATCATTAAATATTA
1 AATCATT-AATATCA
*
1681 AATCATT-A-CT-A
1 AATCATTAATATCA
1692 AATCATTAATATCA
1 AATCATTAATATCA
1706 AATCATTAAATATCA
1 AATCATT-AATATCA
1721 AATCATTGTTCAAGTAGT-A
1 AATCA---TT-AA-TA-TCA
*
1740 AATCATTACTATCA
1 AATCATTAATATCA
*
1754 AATCATT-A-CT-A
1 AATCATTAATATCA
1765 AATCATTAATATCA
1 AATCATTAATATCA
1779 AATCATTAA
1 AATCATTAA
1788 ATATTAATAA
Statistics
Matches: 87, Mismatches: 7, Indels: 27
0.72 0.06 0.22
Matches are distributed among these distances:
11 16 0.18
12 4 0.05
13 4 0.05
14 28 0.32
15 20 0.23
16 2 0.02
18 4 0.05
19 8 0.09
20 1 0.01
ACGTcount: A:0.48, C:0.14, G:0.02, T:0.36
Consensus pattern (14 bp):
AATCATTAATATCA
Found at i:1827 original size:60 final size:60
Alignment explanation
Indices: 1754--1888 Score: 252
Period size: 60 Copynumber: 2.2 Consensus size: 60
1744 ATTACTATCA
*
1754 AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACT
1 AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATCATTACT
*
1814 AATCATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATCATTACT
1 AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATCATTACT
1874 AATCATTACTAAATC
1 AATCATTACTAAATC
1889 TTATAAATAC
Statistics
Matches: 73, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
60 73 1.00
ACGTcount: A:0.46, C:0.14, G:0.00, T:0.40
Consensus pattern (60 bp):
AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATCATTACT
Found at i:9025 original size:33 final size:33
Alignment explanation
Indices: 8983--9057 Score: 141
Period size: 33 Copynumber: 2.3 Consensus size: 33
8973 CTTGTAGGTA
8983 GTGCATGGCGACCTGTGTTGGGGTGCTGGGGAC
1 GTGCATGGCGACCTGTGTTGGGGTGCTGGGGAC
*
9016 GTGCATGGCGACCTGTGTTGGGGTGTTGGGGAC
1 GTGCATGGCGACCTGTGTTGGGGTGCTGGGGAC
9049 GTGCATGGC
1 GTGCATGGC
9058 ACATGCAGAC
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.09, C:0.17, G:0.48, T:0.25
Consensus pattern (33 bp):
GTGCATGGCGACCTGTGTTGGGGTGCTGGGGAC
Found at i:10566 original size:21 final size:21
Alignment explanation
Indices: 10540--10582 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
10530 CAATGTAGTT
10540 AATTACTTCTTGCTGCCATTG
1 AATTACTTCTTGCTGCCATTG
10561 AATTACTTCTTGCTGCCATTG
1 AATTACTTCTTGCTGCCATTG
10582 A
1 A
10583 TTCTAGTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.21, C:0.23, G:0.14, T:0.42
Consensus pattern (21 bp):
AATTACTTCTTGCTGCCATTG
Found at i:11067 original size:24 final size:24
Alignment explanation
Indices: 11040--11097 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 24
11030 TTTTATGTTC
* *
11040 GTTCGTTTATATTC-GTCTGTTTGT
1 GTTCGTTTATATTCATTC-ATTTGT
* *
11064 GTTCATTTACATTCATTCATTTGT
1 GTTCGTTTATATTCATTCATTTGT
11088 GTTCGTTTAT
1 GTTCGTTTAT
11098 CATTTAAACG
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
24 25 0.93
25 2 0.07
ACGTcount: A:0.14, C:0.14, G:0.16, T:0.57
Consensus pattern (24 bp):
GTTCGTTTATATTCATTCATTTGT
Found at i:14105 original size:27 final size:28
Alignment explanation
Indices: 14075--14130 Score: 80
Period size: 27 Copynumber: 2.0 Consensus size: 28
14065 AATCACTCTT
*
14075 GATATATCTGAATCC-TAAAT-ATCCTAA
1 GATATAACTGAA-CCTTAAATGATCCTAA
14102 GATATAACTGAACCTTAAATGATCCTAA
1 GATATAACTGAACCTTAAATGATCCTAA
14130 G
1 G
14131 GTATTTATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
26 2 0.08
27 16 0.62
28 8 0.31
ACGTcount: A:0.41, C:0.18, G:0.11, T:0.30
Consensus pattern (28 bp):
GATATAACTGAACCTTAAATGATCCTAA
Found at i:14751 original size:61 final size:60
Alignment explanation
Indices: 14539--14802 Score: 271
Period size: 60 Copynumber: 4.4 Consensus size: 60
14529 GGACGATCCC
* * * * * ** * * * * *
14539 TTTGCTTTGTACATTAGGTAATTCTTTATAGACCAAGGGACACTCTCATCAGGGGGCTCA
1 TTTGCTTTGTGCATTGGGTAAGTCCTTATGGACCTGGGGGCACTCCCCTCAGGTGTCTCA
*
14599 TTTGCGTTGTGCATTGGGTAAGTCCTTATGGACCTGGGGGCACTCCCCTCAGGTGTCTCA
1 TTTGCTTTGTGCATTGGGTAAGTCCTTATGGACCTGGGGGCACTCCCCTCAGGTGTCTCA
* * * * * *
14659 TTTCCTTTGTGCATTGGGTAAGTCCTTATGGACTTGGGGGAACTACCCTCAGGCATTTCT-T
1 TTTGCTTTGTGCATTGGGTAAGTCCTTATGGACCTGGGGGCACTCCCCTCAGG--TGTCTCA
* * *
14720 TTTGCTTTGTGCATTGGGAAAGTTCTTATGGACCTGGGGGCACTCCCCTCAGGTGACTTC-
1 TTTGCTTTGTGCATTGGGTAAGTCCTTATGGACCTGGGGGCACTCCCCTCAGGTGTC-TCA
* *
14780 TTCGCTTTGTGCATTAGGTAAGT
1 TTTGCTTTGTGCATTGGGTAAGT
14803 TTGTATGGAT
Statistics
Matches: 169, Mismatches: 31, Indels: 8
0.81 0.15 0.04
Matches are distributed among these distances:
59 2 0.01
60 116 0.69
61 47 0.28
62 4 0.02
ACGTcount: A:0.17, C:0.22, G:0.26, T:0.35
Consensus pattern (60 bp):
TTTGCTTTGTGCATTGGGTAAGTCCTTATGGACCTGGGGGCACTCCCCTCAGGTGTCTCA
Found at i:22564 original size:19 final size:19
Alignment explanation
Indices: 22542--22580 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
22532 GTTTGTCTCT
22542 AGGTACTTAGTGTGTCAGC
1 AGGTACTTAGTGTGTCAGC
22561 AGGTACTTAGTGTGTCAGC
1 AGGTACTTAGTGTGTCAGC
22580 A
1 A
22581 AGTTAAGGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.23, C:0.15, G:0.31, T:0.31
Consensus pattern (19 bp):
AGGTACTTAGTGTGTCAGC
Found at i:25371 original size:30 final size:30
Alignment explanation
Indices: 25335--25392 Score: 107
Period size: 30 Copynumber: 1.9 Consensus size: 30
25325 AGTTGGTTCA
25335 TGCATATATTTTATCTTTATCATCACTTTG
1 TGCATATATTTTATCTTTATCATCACTTTG
*
25365 TGCATATATTTTATCTTTATTATCACTT
1 TGCATATATTTTATCTTTATCATCACTT
25393 AAAAATATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.24, C:0.16, G:0.05, T:0.55
Consensus pattern (30 bp):
TGCATATATTTTATCTTTATCATCACTTTG
Found at i:30773 original size:54 final size:54
Alignment explanation
Indices: 30297--30762 Score: 575
Period size: 54 Copynumber: 8.6 Consensus size: 54
30287 CTATGTGTAC
* *
30297 TATATGCACTAAGTGTGCAACCCACAAAATTCATCATATGTTGATGAACGACCT
1 TATAGGCACTAAGTGTGCAACCCACAGAATTCATCATATGTTGATGAACGACCT
* * *
30351 TATAGGCACTAAGTGTTCAACCCACAGAATTCATCATATGTTGATGAATGACCG
1 TATAGGCACTAAGTGTGCAACCCACAGAATTCATCATATGTTGATGAACGACCT
* * *
30405 TATAGGCACTAAGTGTGTAACCCACGGAATTCATCATATGTTGATGAACGACCG
1 TATAGGCACTAAGTGTGCAACCCACAGAATTCATCATATGTTGATGAACGACCT
* * *
30459 TATAGGCACTAAGTGTGCAACCCACAAAATTCATCATATGTTAATGGACGA-CT
1 TATAGGCACTAAGTGTGCAACCCACAGAATTCATCATATGTTGATGAACGACCT
* * * *
30512 GTATAGGCACTAAGTGGGTAACCCACAAAATTCATCATATATTGATGAACGA-CT
1 -TATAGGCACTAAGTGTGCAACCCACAGAATTCATCATATGTTGATGAACGACCT
*
30566 GTATAGGCACTAAGTGTGCAACCCAC-GAAATTCATCATATGTTGATGAACGATCT
1 -TATAGGCACTAAGTGTGCAACCCACAG-AATTCATCATATGTTGATGAACGACCT
* * * *
30621 TATAGGCACTAAATGTGCAACCCA-TGAAATTCATCATATGTTGATCAACGACCG
1 TATAGGCACTAAGTGTGCAACCCACAG-AATTCATCATATGTTGATGAACGACCT
* * * * * *
30675 TATAGGCACTCAGTGTGCAAACCA-AGGAATTCATAATGTGTTTATGAATGACCT
1 TATAGGCACTAAGTGTGCAACCCACA-GAATTCATCATATGTTGATGAACGACCT
* **
30729 TATCA-GCACTAAGTGTGCAATCCATTGAATTCAT
1 TAT-AGGCACTAAGTGTGCAACCCACAGAATTCAT
30763 AATTTGTTTA
Statistics
Matches: 364, Mismatches: 41, Indels: 14
0.87 0.10 0.03
Matches are distributed among these distances:
53 1 0.00
54 359 0.99
55 4 0.01
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.27
Consensus pattern (54 bp):
TATAGGCACTAAGTGTGCAACCCACAGAATTCATCATATGTTGATGAACGACCT
Found at i:35782 original size:54 final size:54
Alignment explanation
Indices: 35700--36110 Score: 444
Period size: 54 Copynumber: 7.6 Consensus size: 54
35690 TAGATGTATA
* * * * *
35700 TTGATGAACGACCATATAGGAACCAAGTGAGCAACCCATGGAATTCATCATATG
1 TTGATGAACGACCGTATAGGCACTAAGTGTGCAACCCACGGAATTCATCATATG
* **
35754 TTGATGAACGACTGTATAGGCACTAAGTGTGCAACCCACAAAATTCATCATATG
1 TTGATGAACGACCGTATAGGCACTAAGTGTGCAACCCACGGAATTCATCATATG
* ** * *
35808 TTGATGGATTACCGTATAGGCACTAAGTGGGCAACCCACGAAATTCATCATATG
1 TTGATGAACGACCGTATAGGCACTAAGTGTGCAACCCACGGAATTCATCATATG
* *
35862 TTGATGAACGATCGTATAGGCACTAAGTGTGCAACCCATGGAATTCATCATATG
1 TTGATGAACGACCGTATAGGCACTAAGTGTGCAACCCACGGAATTCATCATATG
** *
35916 TTGATGAACGACCGTATATTCACTAAATGTGCAACCCACGGAATTCATCATATG
1 TTGATGAACGACCGTATAGGCACTAAGTGTGCAACCCACGGAATTCATCATATG
* * ** ** *
35970 TTGATGAACGACCGTGTAGGCACTAAGTGTGCAAACCACAAAATTCAAAATGTG
1 TTGATGAACGACCGTATAGGCACTAAGTGTGCAACCCACGGAATTCATCATATG
* * * * * * * * *** * *
36024 TTTATGAAGGATCGTATTGGCACCAAGTTTTCAATCCATATAATTCATAATGTG
1 TTGATGAACGACCGTATAGGCACTAAGTGTGCAACCCACGGAATTCATCATATG
* * * *
36078 TTTATGAATGACCGTATCGGCACTACGTGTGCA
1 TTGATGAACGACCGTATAGGCACTAAGTGTGCA
36111 CCCTAGAGAA
Statistics
Matches: 302, Mismatches: 55, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
54 302 1.00
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.27
Consensus pattern (54 bp):
TTGATGAACGACCGTATAGGCACTAAGTGTGCAACCCACGGAATTCATCATATG
Found at i:35967 original size:162 final size:162
Alignment explanation
Indices: 35700--36102 Score: 500
Period size: 162 Copynumber: 2.5 Consensus size: 162
35690 TAGATGTATA
* * * *
35700 TTGATGAACGACCATATAGGAACCAAGTGAGCAACCCATGGAATTCATCATATGTTGATGAACGA
1 TTGATGAACGATCGTATAGGCACCAAGTGTGCAACCCATGGAATTCATCATATGTTGATGAACGA
* * * **
35765 CTGTATAGGCACTAAGTGTGCAACCCACAAAATTCATCATATGTTGATGGATTACCGTATAGGCA
66 CCGTATAGGCACTAAATGTGCAACCCACAAAATTCATCATATGTTGATGAACGACCGTATAGGCA
* * **
35830 CTAAGTGGGCAACCCACGAAATTCATCATATG
131 CTAAGTGGGCAAACCACAAAATTCAAAATATG
*
35862 TTGATGAACGATCGTATAGGCACTAAGTGTGCAACCCATGGAATTCATCATATGTTGATGAACGA
1 TTGATGAACGATCGTATAGGCACCAAGTGTGCAACCCATGGAATTCATCATATGTTGATGAACGA
** ** *
35927 CCGTATATTCACTAAATGTGCAACCCACGGAATTCATCATATGTTGATGAACGACCGTGTAGGCA
66 CCGTATAGGCACTAAATGTGCAACCCACAAAATTCATCATATGTTGATGAACGACCGTATAGGCA
* *
35992 CTAAGTGTGCAAACCACAAAATTCAAAATGTG
131 CTAAGTGGGCAAACCACAAAATTCAAAATATG
* * * * * * ** * * * *
36024 TTTATGAAGGATCGTATTGGCACCAAGTTTTCAATCCATATAATTCATAATGTGTTTATGAATGA
1 TTGATGAACGATCGTATAGGCACCAAGTGTGCAACCCATGGAATTCATCATATGTTGATGAACGA
*
36089 CCGTATCGGCACTA
66 CCGTATAGGCACTA
36103 CGTGTGCACC
Statistics
Matches: 204, Mismatches: 37, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
162 204 1.00
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.27
Consensus pattern (162 bp):
TTGATGAACGATCGTATAGGCACCAAGTGTGCAACCCATGGAATTCATCATATGTTGATGAACGA
CCGTATAGGCACTAAATGTGCAACCCACAAAATTCATCATATGTTGATGAACGACCGTATAGGCA
CTAAGTGGGCAAACCACAAAATTCAAAATATG
Found at i:39419 original size:3 final size:3
Alignment explanation
Indices: 39411--39461 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
39401 TTGTAAAAGC
39411 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
39459 ATA
1 ATA
39462 GTAGTAGTAA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:41929 original size:29 final size:28
Alignment explanation
Indices: 41897--41978 Score: 119
Period size: 29 Copynumber: 2.8 Consensus size: 28
41887 GTATCTATTA
*
41897 TAATTTATAAAAGGTTTTATCTTTAATTT
1 TAATTTATAAAA-GTTTTATCCTTAATTT
41926 TAATTTATAAAAAGTTTTATCCTTAATTT
1 TAATTTAT-AAAAGTTTTATCCTTAATTT
*
41955 TAATTTATATAAAGTTTTGTCCTT
1 TAATTTATA-AAAGTTTTATCCTT
41979 TTACTAAAAT
Statistics
Matches: 49, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
28 1 0.02
29 44 0.90
30 4 0.08
ACGTcount: A:0.34, C:0.06, G:0.06, T:0.54
Consensus pattern (28 bp):
TAATTTATAAAAGTTTTATCCTTAATTT
Found at i:41959 original size:58 final size:56
Alignment explanation
Indices: 41860--41972 Score: 133
Period size: 58 Copynumber: 2.0 Consensus size: 56
41850 AACCTTTCTC
41860 CTTTAATGTAATTTATAAAAAGTTGTGGTATCTATTATAATTTATA-AAAGGTTTTAT
1 CTTTAATGTAATTTATAAAAAGTTGT-GTATCTATTATAATTTATATAAA-GTTTTAT
* *
41917 CTTTAATTTTAATTTATAAAAAGTT-T-TATCCTTAATTTTAATTTATATAAAGTTTT
1 CTTTAA-TGTAATTTATAAAAAGTTGTGTAT-C-T-ATTATAATTTATATAAAGTTTT
41973 GTCCTTTTAC
Statistics
Matches: 49, Mismatches: 2, Indels: 9
0.82 0.03 0.15
Matches are distributed among these distances:
55 3 0.06
56 1 0.02
57 8 0.16
58 34 0.69
59 3 0.06
ACGTcount: A:0.36, C:0.04, G:0.08, T:0.51
Consensus pattern (56 bp):
CTTTAATGTAATTTATAAAAAGTTGTGTATCTATTATAATTTATATAAAGTTTTAT
Found at i:42022 original size:26 final size:26
Alignment explanation
Indices: 41992--42042 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
41982 CTAAAATGTT
* *
41992 TTGTCCTTTAGTGTAATTTATAAAAG
1 TTGTCCTTAAATGTAATTTATAAAAG
*
42018 TTGTCCTTAAATGTGATTTATAAAA
1 TTGTCCTTAAATGTAATTTATAAAA
42043 AAGTTGTGTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.33, C:0.08, G:0.14, T:0.45
Consensus pattern (26 bp):
TTGTCCTTAAATGTAATTTATAAAAG
Found at i:46236 original size:37 final size:37
Alignment explanation
Indices: 46146--46250 Score: 129
Period size: 37 Copynumber: 2.8 Consensus size: 37
46136 CCTTTTCGTC
* *
46146 CTACTAGGATTTAAACTCCTAAAAATAGGATATAATT
1 CTACTAGGATTTAAACTCCTAAAAATATGATAGAATT
* * * *
46183 TTGCTAGGATTCAAACTCCTAAAAATATGATAGAGTT
1 CTACTAGGATTTAAACTCCTAAAAATATGATAGAATT
** *
46220 CTACTATTATTTAAACTCCTAAAGATATGAT
1 CTACTAGGATTTAAACTCCTAAAAATATGAT
46251 CCACAAGCAC
Statistics
Matches: 56, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
37 56 1.00
ACGTcount: A:0.40, C:0.14, G:0.11, T:0.34
Consensus pattern (37 bp):
CTACTAGGATTTAAACTCCTAAAAATATGATAGAATT
Found at i:46767 original size:20 final size:20
Alignment explanation
Indices: 46742--46779 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
46732 ATTATTATTA
46742 TTTTACTTATATATATATGC
1 TTTTACTTATATATATATGC
* *
46762 TTTTACTTTTTTATATAT
1 TTTTACTTATATATATAT
46780 TTTACTCATT
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:0.26, C:0.08, G:0.03, T:0.63
Consensus pattern (20 bp):
TTTTACTTATATATATATGC
Found at i:51475 original size:8 final size:8
Alignment explanation
Indices: 51462--51530 Score: 50
Period size: 8 Copynumber: 8.4 Consensus size: 8
51452 CAATCAGAAC
51462 AAAAACAA
1 AAAAACAA
51470 AAAAAC-A
1 AAAAACAA
*
51477 AAAAAGAA
1 AAAAACAA
* *
51485 AAGAAGAA
1 AAAAACAA
*
51493 AAAAAGAA
1 AAAAACAA
*
51501 GAAAACAA
1 AAAAACAA
*
51509 AAGAAAAAA
1 AA-AAACAA
51518 GAAAGAACAA
1 -AAA-AACAA
51528 AAA
1 AAA
51531 TCAAAAAGAA
Statistics
Matches: 49, Mismatches: 8, Indels: 7
0.77 0.12 0.11
Matches are distributed among these distances:
7 6 0.12
8 28 0.57
9 9 0.18
10 6 0.12
ACGTcount: A:0.83, C:0.06, G:0.12, T:0.00
Consensus pattern (8 bp):
AAAAACAA
Found at i:51495 original size:24 final size:24
Alignment explanation
Indices: 51463--51543 Score: 74
Period size: 24 Copynumber: 3.2 Consensus size: 24
51453 AATCAGAACA
*
51463 AAAACAAAAAAACAAAAAAGAAAAG
1 AAAA-AAAAAAACAAAAAACAAAAG
* *
51488 AAGAAAAAAAGA-AGAAAACAAAAG
1 AA-AAAAAAAAACAAAAAACAAAAG
*
51512 AAAAAAGAAAGAACAAAAATCAAAAAG
1 AAAAAA-AAA-AACAAAAAAC-AAAAG
51539 AAAAA
1 AAAAA
51544 GGGACAAAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
23 4 0.09
24 15 0.33
25 9 0.20
26 7 0.16
27 10 0.22
ACGTcount: A:0.81, C:0.06, G:0.11, T:0.01
Consensus pattern (24 bp):
AAAAAAAAAAACAAAAAACAAAAG
Found at i:51499 original size:11 final size:11
Alignment explanation
Indices: 51468--51530 Score: 58
Period size: 11 Copynumber: 5.6 Consensus size: 11
51458 GAACAAAAAC
* *
51468 AAAAAAACAAA
1 AAAAAAAGAAG
51479 AAAGAAAAGAAG
1 AAA-AAAAGAAG
51491 AAAAAAAGAAG
1 AAAAAAAGAAG
*
51502 AAAACAA-AAG
1 AAAAAAAGAAG
51512 -AAAAAAGAAAG
1 AAAAAAAG-AAG
51523 AACAAAAA
1 AA-AAAAA
51531 TCAAAAAGAA
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
9 5 0.12
10 3 0.07
11 20 0.47
12 10 0.23
13 5 0.12
ACGTcount: A:0.83, C:0.05, G:0.13, T:0.00
Consensus pattern (11 bp):
AAAAAAAGAAG
Found at i:51530 original size:20 final size:19
Alignment explanation
Indices: 51465--51530 Score: 64
Period size: 21 Copynumber: 3.4 Consensus size: 19
51455 TCAGAACAAA
*
51465 AACAAAAA-AACAAAAAAG
1 AACAAAAAGAAAAAAAAAG
*
51483 AA-AAGAAGAAAAAAAGAAG
1 AACAAAAAGAAAAAAA-AAG
*
51502 AAAACAAAAGAAAAAAGAAAG
1 AACA-AAAAGAAAAAA-AAAG
51523 AACAAAAA
1 AACAAAAA
51531 TCAAAAAGAA
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
17 4 0.10
18 8 0.21
19 5 0.13
20 5 0.13
21 16 0.41
22 1 0.03
ACGTcount: A:0.82, C:0.06, G:0.12, T:0.00
Consensus pattern (19 bp):
AACAAAAAGAAAAAAAAAG
Found at i:51543 original size:7 final size:7
Alignment explanation
Indices: 51469--51543 Score: 55
Period size: 7 Copynumber: 10.7 Consensus size: 7
51459 AACAAAAACA
*
51469 AAAAAAC
1 AAAAAAG
51476 AAAAAAG
1 AAAAAAG
51483 AAAAGAAG
1 AAAA-AAG
51491 AAAAAAAG
1 -AAAAAAG
*
51499 AAGAAA-
1 AAAAAAG
*
51505 ACAAAAG
1 AAAAAAG
51512 AAAAAAG
1 AAAAAAG
*
51519 AAAGAA-
1 AAAAAAG
* *
51525 CAAAAAT
1 AAAAAAG
*
51532 CAAAAAG
1 AAAAAAG
51539 AAAAA
1 AAAAA
51544 GGGACAAAAA
Statistics
Matches: 54, Mismatches: 10, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
6 8 0.15
7 36 0.67
8 6 0.11
9 4 0.07
ACGTcount: A:0.81, C:0.05, G:0.12, T:0.01
Consensus pattern (7 bp):
AAAAAAG
Found at i:52177 original size:22 final size:22
Alignment explanation
Indices: 52149--52203 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
52139 GCTACCCCAT
52149 CAAACCTTTGAGCATCAAATGG
1 CAAACCTTTGAGCATCAAATGG
*
52171 CAAACCTTTGAGCATCAAATGT
1 CAAACCTTTGAGCATCAAATGG
*
52193 AAAACCTTTGA
1 CAAACCTTTGA
52204 CCAAACACAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.38, C:0.22, G:0.15, T:0.25
Consensus pattern (22 bp):
CAAACCTTTGAGCATCAAATGG
Found at i:52641 original size:18 final size:19
Alignment explanation
Indices: 52618--52654 Score: 67
Period size: 18 Copynumber: 2.0 Consensus size: 19
52608 TCAACATCAA
52618 ATATTGGGGCATT-TTTGG
1 ATATTGGGGCATTATTTGG
52636 ATATTGGGGCATTATTTGG
1 ATATTGGGGCATTATTTGG
52655 GGATTCAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.19, C:0.05, G:0.32, T:0.43
Consensus pattern (19 bp):
ATATTGGGGCATTATTTGG
Found at i:53244 original size:106 final size:104
Alignment explanation
Indices: 53028--53554 Score: 663
Period size: 106 Copynumber: 5.0 Consensus size: 104
53018 ATATCTTGCA
* * * * *
53028 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGATGGCTGGTTGTCAACAATAATTTTCCA
1 ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACGGCTGGTTGTCAAAAACAA-TTTCCA
* *
53093 ATTTCGGAGCCAATTTCAACTTCACAGCGAATGATATTGG
65 ATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
53133 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACGGCTGGTTGTCAA-AAACAATTT-CC
* *
53198 AATTTCAGATCCAATTTCAACTTCAAAGCGAAGGATATTGG
64 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
53239 ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTTCT
1 ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACGGCTGGTTGTCAA-AAACAA-TTTCC
* * *
53304 AATTTCAGAGCTAATTTCAACTTCTCAGCGAAGGATCTTGG
64 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * *
53345 AC-CCAAGACAACACAAGCTCAACTTCACGACAAAGGGGCGGCTGATTGTCAACAA-AATTT-C-
1 ACTCC-AGACAACACAAGTTCAACTTCACGACGAAGGGACGGCTGGTTGTCAAAAACAATTTCCA
*
53406 A-TTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGG
65 ATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
53445 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCC
1 ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACGGCTGGTTGTCAA-AAACAATTT-CC
** * *
53510 GGTTCCAGAGCCAATTTCAACTGCAC-GAC-AGAGGATATTGG
64 AATTTCAGAGCCAATTTCAACTTCACAG-CGA-AGGATATTGG
53551 ACTC
1 ACTC
53555 GGAACAATGC
Statistics
Matches: 369, Mismatches: 40, Indels: 25
0.85 0.09 0.06
Matches are distributed among these distances:
100 78 0.21
101 4 0.01
102 5 0.01
103 3 0.01
104 3 0.01
105 56 0.15
106 217 0.59
107 3 0.01
ACGTcount: A:0.34, C:0.24, G:0.19, T:0.23
Consensus pattern (104 bp):
ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACGGCTGGTTGTCAAAAACAATTTCCAA
TTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
Found at i:53462 original size:206 final size:209
Alignment explanation
Indices: 53028--53554 Score: 676
Period size: 206 Copynumber: 2.5 Consensus size: 209
53018 ATATCTTGCA
* * *
53028 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGATGGCTGGTTGTCAACAATAATTTTCCA
1 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAAAAACAA-TTTCCA
* * * *
53093 ATTTCGGAGCCAATTTCAACTTCACAGCGAATGATATTGGACTCCAGACAACGCAAGTTCAACTT
65 ATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACACAAGCTCAACTT
* *
53158 CACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGATCCAATTTCAACTTCA
130 CACGACAAAGGGACCGCTGATTGTCAATAAACAATTT-CCAATTTCAGATCCAATTTCAACTTCA
53223 AAGCGAAGGATATTGG
194 AAGCGAAGGATATTGG
* * * *
53239 ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTTCT
1 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAA-AAACAA-TTTCC
* * *
53304 AATTTCAGAGCTAATTTCAACTTCTCAGCGAAGGATCTTGGAC-CCAAGACAACACAAGCTCAAC
64 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCC-AGACAACACAAGCTCAAC
* * *
53368 TTCACGACAAAGGGGCGGCTGATTGTCAA-CAA-AATTT-C-A-TTCAGAGT-CAATTTCAACTT
128 TTCACGACAAAGGGACCGCTGATTGTCAATAAACAATTTCCAATTTCAGA-TCCAATTTCAACTT
*
53427 CACAGCGAAGGATATTGG
192 CAAAGCGAAGGATATTGG
*
53445 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCC
1 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAA-AAACAATTT-CC
** * *
53510 GGTTCCAGAGCCAATTTCAACTGCAC-GAC-AGAGGATATTGGACTC
64 AATTTCAGAGCCAATTTCAACTTCACAG-CGA-AGGATATTGGACTC
53555 GGAACAATGC
Statistics
Matches: 276, Mismatches: 33, Indels: 18
0.84 0.10 0.06
Matches are distributed among these distances:
205 5 0.02
206 123 0.45
207 3 0.01
208 1 0.00
210 5 0.02
211 52 0.19
212 87 0.32
ACGTcount: A:0.34, C:0.24, G:0.19, T:0.23
Consensus pattern (209 bp):
ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAAAAACAATTTCCAA
TTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACACAAGCTCAACTTC
ACGACAAAGGGACCGCTGATTGTCAATAAACAATTTCCAATTTCAGATCCAATTTCAACTTCAAA
GCGAAGGATATTGG
Found at i:54336 original size:37 final size:37
Alignment explanation
Indices: 54285--54389 Score: 138
Period size: 37 Copynumber: 2.8 Consensus size: 37
54275 CCTTTTTGTC
*
54285 CTACTAGGATTCAAACTCCTAAAAATAGGATATAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* * *
54322 TTACTAGGATTCAAACTCCTAAAAGTAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
** * *
54359 CTACTATTATTTAAACTCCTAAAGATAGGAT
1 CTACTAGGATTCAAACTCCTAAAAATAGGAT
54390 CCACAAGCAC
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 58 1.00
ACGTcount: A:0.40, C:0.15, G:0.13, T:0.31
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
Found at i:55114 original size:16 final size:18
Alignment explanation
Indices: 55074--55114 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
55064 TATTGTATTT
*
55074 TTTATTTTATATATTCCA
1 TTTATTTTATATATTACA
*
55092 TTCATTTTATAT-TTAC-
1 TTTATTTTATATATTACA
55108 TTTATTT
1 TTTATTT
55115 CTTTCTTAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
16 6 0.30
17 3 0.15
18 11 0.55
ACGTcount: A:0.24, C:0.10, G:0.00, T:0.66
Consensus pattern (18 bp):
TTTATTTTATATATTACA
Found at i:57961 original size:27 final size:26
Alignment explanation
Indices: 57896--57962 Score: 75
Period size: 27 Copynumber: 2.6 Consensus size: 26
57886 TAAATAATAT
*
57896 TAATTAAATT-AAAATTTTAAAATTA
1 TAATTAAATTAAAAATTTCAAAATTA
**
57921 T-ATTGAAACAAAAAATTTCCAAAATTA
1 TAATT-AAATTAAAAATTT-CAAAATTA
57948 TAATTAAATTAAAAA
1 TAATTAAATTAAAAA
57963 ATATTCTTTC
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
24 3 0.09
25 4 0.12
26 7 0.21
27 16 0.48
28 3 0.09
ACGTcount: A:0.58, C:0.04, G:0.01, T:0.36
Consensus pattern (26 bp):
TAATTAAATTAAAAATTTCAAAATTA
Found at i:61783 original size:62 final size:61
Alignment explanation
Indices: 61673--61932 Score: 345
Period size: 62 Copynumber: 4.3 Consensus size: 61
61663 AATGACCAAC
* * * * *
61673 AAAATCGCAACGCGATAT-CAA-AACCGCAACGCGATTTAA-AAAAGCGCAACGTTGA-AAAG
1 AAAATCGCAACGCGATTTCCAAGAATCGCAACGCGA-TTAAGAAAATCGCAACG-CGATTAAG
* *
61732 AAGATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTCAGAAAATCGCAACGCGATTCCAAG
1 AAAATCGCAACGCGAT-TTCCAAGAATCGCAACGCGATTAAGAAAATCGCAACGCGATT--AAG
61796 --AATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTAAGAAAATCGCAACGCGATTAAG
1 AAAATCGCAACGCGAT-TTCCAAGAATCGCAACGCGATTAAGAAAATCGCAACGCGATTAAG
*
61856 AAAATCGCAACGCGA-TTCCAAGAATCGCAACGCGATTAAGATAATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTTCCAAGAATCGCAACGCGATTAAGAAAATCGCAACGCGATTAAG
61916 AAAATCGCAACGCGATT
1 AAAATCGCAACGCGATT
61933 CAGAAAATGA
Statistics
Matches: 181, Mismatches: 10, Indels: 18
0.87 0.05 0.09
Matches are distributed among these distances:
59 15 0.08
60 63 0.35
61 9 0.05
62 91 0.50
64 3 0.02
ACGTcount: A:0.40, C:0.25, G:0.20, T:0.16
Consensus pattern (61 bp):
AAAATCGCAACGCGATTTCCAAGAATCGCAACGCGATTAAGAAAATCGCAACGCGATTAAG
Found at i:61937 original size:20 final size:20
Alignment explanation
Indices: 61673--61940 Score: 244
Period size: 20 Copynumber: 13.2 Consensus size: 20
61663 AATGACCAAC
61673 AAAATCGCAACGCGATATC--
1 AAAATCGCAACGCGAT-TCAG
* * *
61692 AAAACCGCAACGCGATTTAA
1 AAAATCGCAACGCGATTCAG
* * **
61712 AAAAGCGCAACGTTGA-AAAG
1 AAAATCGCAACG-CGATTCAG
*
61732 AAGATCGCAACGCGATCTTCCA-
1 AAAATCGCAACGCGA--TT-CAG
*
61754 AGAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTCAG
61774 AAAATCGCAACGCGATTCCA-
1 AAAATCGCAACGCGATT-CAG
*
61794 AGAATCGCAACGCGATCTTCCA-
1 AAAATCGCAACGCGA--TT-CAG
* *
61816 AGAATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTCAG
*
61836 AAAATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTCAG
61856 AAAATCGCAACGCGATTCCA-
1 AAAATCGCAACGCGATT-CAG
* *
61876 AGAATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTCAG
* *
61896 ATAATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTCAG
61916 AAAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTCAG
61936 AAAAT
1 AAAAT
61941 GAGTAAATTC
Statistics
Matches: 211, Mismatches: 24, Indels: 27
0.81 0.09 0.10
Matches are distributed among these distances:
18 1 0.00
19 21 0.10
20 150 0.71
21 5 0.02
22 33 0.16
23 1 0.00
ACGTcount: A:0.41, C:0.24, G:0.19, T:0.16
Consensus pattern (20 bp):
AAAATCGCAACGCGATTCAG
Found at i:62047 original size:6 final size:6
Alignment explanation
Indices: 62036--62108 Score: 123
Period size: 6 Copynumber: 12.5 Consensus size: 6
62026 GACACGTATT
62036 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
*
62084 ACCACG ACCCCG ACC-CG ACC-CG ACC
1 ACCACG ACCACG ACCACG ACCACG ACC
62109 CGAGACGAGA
Statistics
Matches: 66, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
5 10 0.15
6 56 0.85
ACGTcount: A:0.30, C:0.53, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:63793 original size:58 final size:57
Alignment explanation
Indices: 63730--63929 Score: 242
Period size: 58 Copynumber: 3.5 Consensus size: 57
63720 TCAAGAAAAT
* *
63730 AACAATTTATTTTCCTTACAAAGTTAAAATAATTCAAGATTTCTATGGAAATAAATTC
1 AACAATCTATTTTCCTTACAAAGTTAAAATAATTTAAGA-TTCTATGGAAATAAATTC
* * *
63788 AACAATTTA-TTTCCTTTACAAAGTTAAAATTATTTAAGATTCTCAAGGAAATAAATTC
1 AACAATCTATTTTCC-TTACAAAGTTAAAATAATTTAAGATTCT-ATGGAAATAAATTC
* * * * *
63846 AACAATCTATTTTCCTTACAAATTTAGAATCATTTTAGAGTCT-TAGAGAAATAAATTC
1 AACAATCTATTTTCCTTACAAAGTTAAAATAATTTAAGATTCTAT-G-GAAATAAATTC
*
63904 AACAATCTATCTTCCTTACAAAGTTA
1 AACAATCTATTTTCCTTACAAAGTTA
63930 GAATCAACGC
Statistics
Matches: 125, Mismatches: 12, Indels: 10
0.85 0.08 0.07
Matches are distributed among these distances:
57 10 0.08
58 110 0.88
59 5 0.04
ACGTcount: A:0.41, C:0.14, G:0.07, T:0.38
Consensus pattern (57 bp):
AACAATCTATTTTCCTTACAAAGTTAAAATAATTTAAGATTCTATGGAAATAAATTC
Found at i:64165 original size:45 final size:46
Alignment explanation
Indices: 64117--64264 Score: 162
Period size: 45 Copynumber: 3.3 Consensus size: 46
64107 TTTAGCTACC
**
64117 CAATAATCAAAAGGAATTAATAATTTGATTTTAATTTTCG-CAATC-
1 CAATAATCAAAAGGAATTAATCCTTTGATTTTAATTTTCGACAA-CA
* * * *
64162 CAATATTCAAAAGGAACTAATCCTTTTATTTTACTTTT-GACAACA
1 CAATAATCAAAAGGAATTAATCCTTTGATTTTAATTTTCGACAACA
* * *
64207 CAATAATCAAAA-GAATTTAATCCTTTGATTTT-ACTTTCGACGACT
1 CAATAATCAAAAGGAA-TTAATCCTTTGATTTTAATTTTCGACAACA
64252 CAATAATCAAAAG
1 CAATAATCAAAAG
64265 TCTTGGATTA
Statistics
Matches: 85, Mismatches: 13, Indels: 9
0.79 0.12 0.08
Matches are distributed among these distances:
44 8 0.09
45 77 0.91
ACGTcount: A:0.41, C:0.16, G:0.08, T:0.36
Consensus pattern (46 bp):
CAATAATCAAAAGGAATTAATCCTTTGATTTTAATTTTCGACAACA
Found at i:70139 original size:36 final size:35
Alignment explanation
Indices: 70093--70166 Score: 130
Period size: 36 Copynumber: 2.1 Consensus size: 35
70083 GGTATGTGGT
70093 TCATCCGACACTGCTCGCAACGAAATTGAGAAAGC
1 TCATCCGACACTGCTCGCAACGAAATTGAGAAAGC
*
70128 TCATCCCGACACTGCTTGCAACGAAATTGAGAAAGC
1 TCAT-CCGACACTGCTCGCAACGAAATTGAGAAAGC
70164 TCA
1 TCA
70167 GGGTAAGGAT
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
35 4 0.11
36 33 0.89
ACGTcount: A:0.34, C:0.28, G:0.19, T:0.19
Consensus pattern (35 bp):
TCATCCGACACTGCTCGCAACGAAATTGAGAAAGC
Found at i:71435 original size:7 final size:7
Alignment explanation
Indices: 71423--71488 Score: 68
Period size: 7 Copynumber: 10.0 Consensus size: 7
71413 GTTGGACGCC
71423 ATTTGCA
1 ATTTGCA
71430 ATTTGCA
1 ATTTGCA
71437 ATTTGCA
1 ATTTGCA
71444 ATTTGCA
1 ATTTGCA
* *
71451 AGTTGGA
1 ATTTGCA
71458 A--TGCA
1 ATTTGCA
71463 ATTTGCA
1 ATTTGCA
* *
71470 AGTTGGA
1 ATTTGCA
71477 A--TGCA
1 ATTTGCA
71482 ATTTGCA
1 ATTTGCA
71489 GATGCAATGG
Statistics
Matches: 49, Mismatches: 6, Indels: 8
0.78 0.10 0.13
Matches are distributed among these distances:
5 8 0.16
7 41 0.84
ACGTcount: A:0.30, C:0.12, G:0.21, T:0.36
Consensus pattern (7 bp):
ATTTGCA
Found at i:71464 original size:19 final size:19
Alignment explanation
Indices: 71440--71488 Score: 98
Period size: 19 Copynumber: 2.6 Consensus size: 19
71430 ATTTGCAATT
71440 TGCAATTTGCAAGTTGGAA
1 TGCAATTTGCAAGTTGGAA
71459 TGCAATTTGCAAGTTGGAA
1 TGCAATTTGCAAGTTGGAA
71478 TGCAATTTGCA
1 TGCAATTTGCA
71489 GATGCAATGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.31, C:0.12, G:0.24, T:0.33
Consensus pattern (19 bp):
TGCAATTTGCAAGTTGGAA
Found at i:81157 original size:98 final size:99
Alignment explanation
Indices: 80988--81189 Score: 325
Period size: 98 Copynumber: 2.1 Consensus size: 99
80978 TGAAAATAAT
* *
80988 ATATTCAGGCTATTAATAAGTGTCCAAATAAAATCAGAAATAACCATTTAACACTATCATATTGA
1 ATATTCAGGCTATTAATAAGTATCCAAATAAAATCAAAAATAACCATTTAACACTATCATATTGA
81053 ATATATTCATGAATTGCAAGTCATACCA-TTTTA
66 ATATATTCATGAATTGCAAGTCATACCATTTTTA
* * * *
81086 ATATTCGGGCTATTAATAAGTATCCGAATAAAATCAAAAATAATCATTTAACATTATCATATTGA
1 ATATTCAGGCTATTAATAAGTATCCAAATAAAATCAAAAATAACCATTTAACACTATCATATTGA
* *
81151 ATATATTCGTGAATTGCAAGTCATATCATTTTTA
66 ATATATTCATGAATTGCAAGTCATACCATTTTTA
81185 ATATT
1 ATATT
81190 TAAATTAAAA
Statistics
Matches: 95, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
98 85 0.89
99 10 0.11
ACGTcount: A:0.41, C:0.13, G:0.09, T:0.36
Consensus pattern (99 bp):
ATATTCAGGCTATTAATAAGTATCCAAATAAAATCAAAAATAACCATTTAACACTATCATATTGA
ATATATTCATGAATTGCAAGTCATACCATTTTTA
Found at i:87229 original size:27 final size:27
Alignment explanation
Indices: 87190--87243 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
87180 TCGGTGCCGG
* *
87190 AGGAGGAGGAGGAGCACGAGAAGAACT
1 AGGAGCAGAAGGAGCACGAGAAGAACT
* *
87217 AGGAGCAGAAGGAGCTCGTGAAGAACT
1 AGGAGCAGAAGGAGCACGAGAAGAACT
87244 GACTCCCGGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.39, C:0.13, G:0.41, T:0.07
Consensus pattern (27 bp):
AGGAGCAGAAGGAGCACGAGAAGAACT
Done.