Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01000024.1 Corchorus capsularis cultivar CVL-1 contig00024, 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: 4074
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.34
Found at i:1008 original size:8 final size:8
Alignment explanation
Indices: 983--1222 Score: 97
Period size: 8 Copynumber: 31.5 Consensus size: 8
973 TGAAATAAAC
*
983 TGAATAAT
1 TGAAGAAT
* *
991 TGATGGAT
1 TGAAGAAT
999 TGAAGAAT
1 TGAAGAAT
* *
1007 TGAATAAG
1 TGAAGAAT
*
1015 TGAAGCAT
1 TGAAGAAT
*
1023 TGAATAAT
1 TGAAGAAT
*
1031 TGAAGTAT
1 TGAAGAAT
1039 TG-A-AAT
1 TGAAGAAT
1045 TGAAGAAT
1 TGAAGAAT
*
1053 TG-A-ATT
1 TGAAGAAT
1059 TGAA-ACAT
1 TGAAGA-AT
1067 TGAA-ACAT
1 TGAAGA-AT
1075 TG-A-AAT
1 TGAAGAAT
1081 ATG-AG-AT
1 -TGAAGAAT
*
1088 TGAAGCAT
1 TGAAGAAT
*
1096 TTAAGAAT
1 TGAAGAAT
1104 TGAAAGAAACAT
1 TG-AAG--A-AT
1116 TGAAGAAT
1 TGAAGAAT
1124 TG-A-AAT
1 TGAAGAAT
*
1130 TGAAGCAT
1 TGAAGAAT
*
1138 TGAAGCAT
1 TGAAGAAT
1146 TGAAGAA-
1 TGAAGAAT
*
1153 TGGA-AAT
1 TGAAGAAT
*
1160 TGAAGCAT
1 TGAAGAAT
*
1168 CGAAGAAT
1 TGAAGAAT
1176 T-AA-AAT
1 TGAAGAAT
*
1182 TGAAGCAT
1 TGAAGAAT
*
1190 TGACA-CAT
1 TGA-AGAAT
1198 TG-A-AAT
1 TGAAGAAT
*
1204 TGAAGCAT
1 TGAAGAAT
1212 TGAA-AAT
1 TGAAGAAT
1219 TGAA
1 TGAA
1223 ATTGAGACAT
Statistics
Matches: 179, Mismatches: 32, Indels: 43
0.70 0.13 0.17
Matches are distributed among these distances:
6 28 0.16
7 33 0.18
8 105 0.59
9 5 0.03
11 4 0.02
12 4 0.02
ACGTcount: A:0.46, C:0.05, G:0.21, T:0.28
Consensus pattern (8 bp):
TGAAGAAT
Found at i:1011 original size:24 final size:23
Alignment explanation
Indices: 983--1141 Score: 74
Period size: 22 Copynumber: 7.2 Consensus size: 23
973 TGAAATAAAC
*
983 TGAATAATTGATGGATTGAAGAAT
1 TGAATAATTGA-GAATTGAAGAAT
* * *
1007 TGAATAAGTGAAGCATTGAATAAT
1 TGAATAATTG-AGAATTGAAGAAT
1031 TGAAGT-ATTGA-AATTGAAGAAT
1 TGAA-TAATTGAGAATTGAAGAAT
*
1053 TGAAT--TTGAAACATTGAA-ACAT
1 TGAATAATTGAGA-ATTGAAGA-AT
*
1075 TG-A-AATATGAG-ATTGAAGCAT
1 TGAATAAT-TGAGAATTGAAGAAT
* *
1096 TTAAGAATTGA-AA--GAA-ACAT
1 TGAATAATTGAGAATTGAAGA-AT
* *
1116 TGAAGAATTGA-AATTGAAGCAT
1 TGAATAATTGAGAATTGAAGAAT
1138 TGAA
1 TGAA
1142 GCATTGAAGA
Statistics
Matches: 107, Mismatches: 12, Indels: 34
0.70 0.08 0.22
Matches are distributed among these distances:
20 21 0.20
21 13 0.12
22 38 0.36
23 7 0.07
24 26 0.24
25 2 0.02
ACGTcount: A:0.46, C:0.04, G:0.21, T:0.30
Consensus pattern (23 bp):
TGAATAATTGAGAATTGAAGAAT
Found at i:1047 original size:14 final size:14
Alignment explanation
Indices: 997--1222 Score: 92
Period size: 14 Copynumber: 15.4 Consensus size: 14
987 TAATTGATGG
997 ATTGAAGAATTGAATA
1 ATTGAAGAATTG-A-A
* *
1013 AGTGAAGCATTGAATA
1 ATTGAAGAATTG-A-A
*
1029 ATTGAAGTATTGAA
1 ATTGAAGAATTGAA
1043 ATTGAAGAATTGAA
1 ATTGAAGAATTGAA
*
1057 TTTGAA-ACATTGAAA
1 ATTGAAGA-ATTG-AA
*
1072 CATTG-A-AATATGAG
1 -ATTGAAGAAT-TGAA
* *
1086 ATTGAAGCATTTAAGA
1 ATTGAAG-AATTGA-A
*
1102 ATTGAAAGAA---AC
1 ATTG-AAGAATTGAA
1114 ATTGAAGAATTGAA
1 ATTGAAGAATTGAA
*
1128 ATTGAAGCATTGAA
1 ATTGAAGAATTGAA
*
1142 GCATTGAAGAATGGAA
1 --ATTGAAGAATTGAA
* *
1158 ATTGAAGCATCGAAGA
1 ATTGAAGAATTG-A-A
1174 ATT-AA-AATTGAA
1 ATTGAAGAATTGAA
*
1186 GCATTGACA-CATTGAA
1 --ATTGA-AGAATTGAA
*
1202 ATTGAAGCATTGAAA
1 ATTGAAGAATTG-AA
1217 ATTGAA
1 ATTGAA
1223 ATTGAGACAT
Statistics
Matches: 166, Mismatches: 22, Indels: 45
0.71 0.09 0.19
Matches are distributed among these distances:
11 5 0.03
12 5 0.03
13 8 0.05
14 67 0.40
15 21 0.13
16 57 0.34
17 3 0.02
ACGTcount: A:0.46, C:0.06, G:0.20, T:0.27
Consensus pattern (14 bp):
ATTGAAGAATTGAA
Found at i:1053 original size:22 final size:21
Alignment explanation
Indices: 1021--1236 Score: 119
Period size: 22 Copynumber: 10.0 Consensus size: 21
1011 TAAGTGAAGC
*
1021 ATTGAATAATTGAAGTATTGAA
1 ATTGAA-AATTGAAGCATTGAA
*
1043 ATTGAAGAATTGAA--TTTGAAA
1 ATTGAA-AATTGAAGCATTG-AA
*
1064 CATTGAAACATTGAA--ATATGAG
1 -ATTGAAA-ATTGAAGCAT-TGAA
* * *
1086 ATTGAAGCATTTAAGAATTGAA
1 ATTGAA-AATTGAAGCATTGAA
*
1108 A--GAAACATTGAAGAATTGAA
1 ATTGAAA-ATTGAAGCATTGAA
*
1128 ATTGAAGCATTGAAGCATTGAA
1 ATTGAA-AATTGAAGCATTGAA
* * *
1150 GAATGGAAATTGAAGCATCGAAGA
1 -ATTGAAAATTGAAGCATTG-A-A
1174 ATT-AAAATTGAAGCATTGACA
1 ATTGAAAATTGAAGCATTGA-A
1195 CATTG-AAATTGAAGCATTGAAA
1 -ATTGAAAATTGAAGCATTG-AA
1217 ATTG-AAATTG-AGACATTGAA
1 ATTGAAAATTGAAG-CATTGAA
1237 TAATGGAGAA
Statistics
Matches: 157, Mismatches: 19, Indels: 38
0.73 0.09 0.18
Matches are distributed among these distances:
20 24 0.15
21 31 0.20
22 89 0.57
23 12 0.08
24 1 0.01
ACGTcount: A:0.46, C:0.06, G:0.20, T:0.28
Consensus pattern (21 bp):
ATTGAAAATTGAAGCATTGAA
Found at i:1114 original size:49 final size:50
Alignment explanation
Indices: 1028--1201 Score: 171
Period size: 52 Copynumber: 3.5 Consensus size: 50
1018 AGCATTGAAT
* * *
1028 AATTGAAGTATTGAA--ATTGAAGAATTGAATTTGAAACATTGAA-ACATTGA
1 AATTGAAGCATTGAAGCATTGAAGAATGGAA--AGAAACATTGAAGA-ATTGA
* *
1078 AATATG-AG-ATTGAAGCATTTAAGAATTGAAAGAAACATTGAAGAATTGA
1 AAT-TGAAGCATTGAAGCATTGAAGAATGGAAAGAAACATTGAAGAATTGA
* * *
1127 AATTGAAGCATTGAAGCATTGAAGAATGGAAATTGAAGCATCGAAGAATTAA
1 AATTGAAGCATTGAAGCATTGAAGAATGGAAA--GAAACATTGAAGAATTGA
1179 AATTGAAGCATTGACA-CATTGAA
1 AATTGAAGCATTGA-AGCATTGAA
1202 ATTGAAGCAT
Statistics
Matches: 108, Mismatches: 7, Indels: 16
0.82 0.05 0.12
Matches are distributed among these distances:
48 2 0.02
49 27 0.25
50 27 0.25
51 15 0.14
52 36 0.33
53 1 0.01
ACGTcount: A:0.47, C:0.06, G:0.20, T:0.27
Consensus pattern (50 bp):
AATTGAAGCATTGAAGCATTGAAGAATGGAAAGAAACATTGAAGAATTGA
Found at i:1138 original size:42 final size:41
Alignment explanation
Indices: 1068--1149 Score: 112
Period size: 42 Copynumber: 2.0 Consensus size: 41
1058 TTGAAACATT
* *
1068 GAAACATTGAAATATGAGATTGAAGCATTTAAGAATTGAAA
1 GAAACATTGAAATATGAAATTGAAGCATTGAAGAATTGAAA
*
1109 GAAACATTGAAGA-ATTGAAATTGAAGCATTGAAGCATTGAA
1 GAAACATTGAA-ATA-TGAAATTGAAGCATTGAAGAATTGAA
1150 GAATGGAAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
41 12 0.33
42 24 0.67
ACGTcount: A:0.48, C:0.06, G:0.21, T:0.26
Consensus pattern (41 bp):
GAAACATTGAAATATGAAATTGAAGCATTGAAGAATTGAAA
Found at i:1149 original size:30 final size:30
Alignment explanation
Indices: 1113--1222 Score: 113
Period size: 30 Copynumber: 3.7 Consensus size: 30
1103 TTGAAAGAAA
1113 CATTGAAGAATTGAAATTGAAGCATTGAAG
1 CATTGAAGAATTGAAATTGAAGCATTGAAG
* *
1143 CATTGAAGAATGGAAATTGAAGCATCGAAG
1 CATTGAAGAATTGAAATTGAAGCATTGAAG
*
1173 AATT-AA-AATTGAAGCATTGACA-CATTGAA-
1 CATTGAAGAATTGAA--ATTGA-AGCATTGAAG
*
1202 -ATTGAAGCATTGAAAATTGAA
1 CATTGAAGAATTG-AAATTGAA
1223 ATTGAGACAT
Statistics
Matches: 68, Mismatches: 6, Indels: 14
0.77 0.07 0.16
Matches are distributed among these distances:
28 10 0.15
29 9 0.13
30 46 0.68
31 3 0.04
ACGTcount: A:0.45, C:0.08, G:0.21, T:0.25
Consensus pattern (30 bp):
CATTGAAGAATTGAAATTGAAGCATTGAAG
Found at i:1222 original size:21 final size:21
Alignment explanation
Indices: 1184--1236 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
1174 ATTAAAATTG
*
1184 AAGCATTGACACATTGAAATTG
1 AAGCATTGA-AAATTGAAATTG
1206 AAGCATTGAAAATTGAAATTG
1 AAGCATTGAAAATTGAAATTG
1227 -AGACATTGAA
1 AAG-CATTGAA
1237 TAATGGAGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
20 2 0.07
21 18 0.62
22 9 0.31
ACGTcount: A:0.45, C:0.09, G:0.19, T:0.26
Consensus pattern (21 bp):
AAGCATTGAAAATTGAAATTG
Found at i:1234 original size:8 final size:7
Alignment explanation
Indices: 1111--1236 Score: 64
Period size: 8 Copynumber: 17.3 Consensus size: 7
1101 AATTGAAAGA
1111 AACATTG
1 AACATTG
*
1118 AAGAATTG
1 AA-CATTG
1126 AA-ATTG
1 AACATTG
1132 AAGCATTG
1 AA-CATTG
1140 AAGCATTG
1 AA-CATTG
* *
1148 AAGAATGG
1 AA-CATTG
1156 AA-ATTG
1 AACATTG
*
1162 AAGCATCG
1 AA-CATTG
*
1170 AAGAATT-
1 AA-CATTG
*
1177 AAAATTG
1 AACATTG
1184 AAGCATTG
1 AA-CATTG
1192 ACACATTG
1 A-ACATTG
1200 AA-ATTG
1 AACATTG
1206 AAGCATTG
1 AA-CATTG
*
1214 AAAATTG
1 AACATTG
1221 AA-ATTG
1 AACATTG
1227 AGACATTG
1 A-ACATTG
1235 AA
1 AA
1237 TAATGGAGAA
Statistics
Matches: 98, Mismatches: 9, Indels: 24
0.75 0.07 0.18
Matches are distributed among these distances:
6 26 0.27
7 15 0.15
8 56 0.57
9 1 0.01
ACGTcount: A:0.46, C:0.08, G:0.21, T:0.25
Consensus pattern (7 bp):
AACATTG
Found at i:1355 original size:22 final size:20
Alignment explanation
Indices: 1325--1608 Score: 148
Period size: 22 Copynumber: 13.2 Consensus size: 20
1315 TCTGGAGATA
*
1325 TGAATTTGAAGCATTGAAACGT
1 TGAAATTGAAGCATTGAAA--T
*
1347 TGAAATTGAAACATTGAAGGAT
1 TGAAATTGAAGCATTGAA--AT
* *
1369 TGAATTTGAAGAATTGAAAT
1 TGAAATTGAAGCATTGAAAT
* *
1389 TAAAACATTGAAGGATT-AAAT
1 T-GAA-ATTGAAGCATTGAAAT
1410 CTGGAGAATTGAA--ATTGAAACAT
1 -T-GA-AATTGAAGCATTG-AA-AT
*
1433 TGAAGGATTGAA--TTTGAGGAAT
1 TGAA--ATTGAAGCATTGA--AAT
1455 TGAAATTGAAGCATTGAAGAAT
1 TGAAATTGAAGCATTG-A-AAT
*
1477 TGAAATTGAAGAATTGAAGAAT
1 TGAAATTGAAGCATTG-A-AAT
*
1499 TGAAATTGAAGCATTGGAAT
1 TGAAATTGAAGCATTGAAAT
*
1519 TGAAATTGAGGC-TTGAAGAAT
1 TGAAATTGAAGCATTG-A-AAT
* *
1540 TGAAATTGAAACACTGTAGAAT
1 TGAAATTGAAGCATTG-A-AAT
** *
1562 TGATTTTGAAGAATTGAAAT
1 TGAAATTGAAGCATTGAAAT
* *
1582 TGAAGCATTGTAGAATTGAAAT
1 TGAA--ATTGAAGCATTGAAAT
1604 TGAAA
1 TGAAA
1609 AATTTTGAAA
Statistics
Matches: 212, Mismatches: 29, Indels: 44
0.74 0.10 0.15
Matches are distributed among these distances:
19 3 0.01
20 34 0.16
21 23 0.11
22 146 0.69
23 5 0.02
24 1 0.00
ACGTcount: A:0.43, C:0.04, G:0.23, T:0.30
Consensus pattern (20 bp):
TGAAATTGAAGCATTGAAAT
Found at i:1378 original size:36 final size:34
Alignment explanation
Indices: 1346--1527 Score: 181
Period size: 36 Copynumber: 5.1 Consensus size: 34
1336 CATTGAAACG
1346 TTGAAATTGAAACATTGAAGGATTGAATTTGAAGAA
1 TTGAAATTGAAACATTGAAGGATTGAATTTG-A-AA
* * *
1382 TTGAAATTAAAACATTGAAGGATTAAATCTGGAGAA
1 TTGAAATTGAAACATTGAAGGATTGAAT-TTGA-AA
1418 TTGAAATTGAAACATTGAAGGATTGAATTTGAGGAA
1 TTGAAATTGAAACATTGAAGGATTGAATTTGA--AA
* * *
1454 TTGAAATTGAAGCATTGAAGAATTGAAATTGAAGAA
1 TTGAAATTGAAACATTGAAGGATTGAATTTG-A-AA
*
1490 TTGAAGAATTG-AA-ATTGAAGCATTGGAA-TTGAAA
1 TTG-A-AATTGAAACATTGAAGGATT-GAATTTGAAA
1524 TTGA
1 TTGA
1528 GGCTTGAAGA
Statistics
Matches: 129, Mismatches: 11, Indels: 15
0.83 0.07 0.10
Matches are distributed among these distances:
33 1 0.01
34 5 0.04
35 4 0.03
36 106 0.82
37 8 0.06
38 5 0.04
ACGTcount: A:0.45, C:0.03, G:0.23, T:0.30
Consensus pattern (34 bp):
TTGAAATTGAAACATTGAAGGATTGAATTTGAAA
Found at i:1398 original size:58 final size:58
Alignment explanation
Indices: 1288--1400 Score: 147
Period size: 58 Copynumber: 1.9 Consensus size: 58
1278 CGTTGACATA
* * * * *
1288 TTGAAATTTAAACATTGAAGAATTGAATCTGGAGATATGAATTTGAAGCATTGAAACG
1 TTGAAATTGAAACATTGAAGAATTGAATCTGAAGATATGAAATTAAAACATTGAAACG
* *
1346 TTGAAATTGAAACATTGAAGGATTGAATTTGAAGA-ATTGAAATTAAAACATTGAA
1 TTGAAATTGAAACATTGAAGAATTGAATCTGAAGATA-TGAAATTAAAACATTGAA
1401 GGATTAAATC
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
57 1 0.02
58 46 0.98
ACGTcount: A:0.44, C:0.05, G:0.19, T:0.31
Consensus pattern (58 bp):
TTGAAATTGAAACATTGAAGAATTGAATCTGAAGATATGAAATTAAAACATTGAAACG
Found at i:1422 original size:72 final size:72
Alignment explanation
Indices: 1346--1519 Score: 237
Period size: 72 Copynumber: 2.4 Consensus size: 72
1336 CATTGAAACG
*
1346 TTGAAATTGAAACATTGAAGGATTGAATTTGAAGAATTGAAATTAAAACATTGAAGGATT-AAAT
1 TTGAAATTGAAACATTGAAGGATTGAATTTGAAGAATTGAAATTAAAACATTGAAGAATTGAAAT
*
1410 CTGGAGAA
66 -TGAAGAA
* * *
1418 TTGAAATTGAAACATTGAAGGATTGAATTTGAGGAATTGAAATTGAAGCATTGAAGAATTGAAAT
1 TTGAAATTGAAACATTGAAGGATTGAATTTGAAGAATTGAAATTAAAACATTGAAGAATTGAAAT
1483 TGAAGAA
66 TGAAGAA
*
1490 TTGAAGAATTG-AA-ATTGAAGCATTGGAATT
1 TTG-A-AATTGAAACATTGAAGGATT-GAATT
1520 GAAATTGAGG
Statistics
Matches: 92, Mismatches: 6, Indels: 7
0.88 0.06 0.07
Matches are distributed among these distances:
72 75 0.82
73 12 0.13
74 5 0.05
ACGTcount: A:0.44, C:0.03, G:0.22, T:0.30
Consensus pattern (72 bp):
TTGAAATTGAAACATTGAAGGATTGAATTTGAAGAATTGAAATTAAAACATTGAAGAATTGAAAT
TGAAGAA
Found at i:1442 original size:8 final size:7
Alignment explanation
Indices: 1417--1549 Score: 75
Period size: 8 Copynumber: 18.9 Consensus size: 7
1407 AATCTGGAGA
1417 ATTGAA-
1 ATTGAAG
*
1423 ATTGAAAC
1 ATTG-AAG
1431 ATTGAAGG
1 ATTGAA-G
1439 ATTGAA-
1 ATTGAAG
* *
1445 TTTGAGG
1 ATTGAAG
1452 AATTGAA-
1 -ATTGAAG
1459 ATTGAAG
1 ATTGAAG
1466 CATTGAAG
1 -ATTGAAG
1474 AATTGAA-
1 -ATTGAAG
1481 ATTGAAG
1 ATTGAAG
1488 AATTGAAG
1 -ATTGAAG
1496 AATTGAA-
1 -ATTGAAG
1503 ATTGAAG
1 ATTGAAG
*
1510 CATTGGA-
1 -ATTGAAG
1517 ATTGAA-
1 ATTGAAG
*
1523 ATTGAGG
1 ATTGAAG
*
1530 CTTGAAG
1 ATTGAAG
1537 AATTGAA-
1 -ATTGAAG
1544 ATTGAA
1 ATTGAA
1550 ACACTGTAGA
Statistics
Matches: 102, Mismatches: 12, Indels: 26
0.73 0.09 0.19
Matches are distributed among these distances:
6 42 0.41
7 9 0.09
8 51 0.50
ACGTcount: A:0.44, C:0.03, G:0.24, T:0.29
Consensus pattern (7 bp):
ATTGAAG
Found at i:1561 original size:63 final size:64
Alignment explanation
Indices: 1450--1607 Score: 188
Period size: 63 Copynumber: 2.6 Consensus size: 64
1440 TTGAATTTGA
* *
1450 GGAATTGAAATTGAAGCATTGAAGAATTGAAATTGAAGAATTGAAGAATTGAAATTGAAGCATT
1 GGAATTGAAATTGAAGCATTGAAGAATTGAAATTGAAGAACTGAAGAATTGAAATTGAAGAATT
* * **
1514 GGAATTGAAATTGAGGC-TTGAAGAATTGAAATTGAA-ACACTGTAGAATTG--ATT-TTGAA--
1 GGAATTGAAATTGAAGCATTGAAGAATTGAAATTGAAGA-ACTGAAGAATTGAAATTGAAGAATT
*
1572 -GAATTGAAATTGAAGCATTGTAGAATTGAAATTGAA
1 GGAATTGAAATTGAAGCATTGAAGAATTGAAATTGAA
1608 AAATTTTGAA
Statistics
Matches: 84, Mismatches: 8, Indels: 10
0.82 0.08 0.10
Matches are distributed among these distances:
57 15 0.18
58 18 0.21
60 2 0.02
61 3 0.04
62 1 0.01
63 29 0.35
64 16 0.19
ACGTcount: A:0.43, C:0.04, G:0.23, T:0.30
Consensus pattern (64 bp):
GGAATTGAAATTGAAGCATTGAAGAATTGAAATTGAAGAACTGAAGAATTGAAATTGAAGAATT
Found at i:1572 original size:36 final size:36
Alignment explanation
Indices: 1531--1600 Score: 122
Period size: 36 Copynumber: 1.9 Consensus size: 36
1521 AAATTGAGGC
1531 TTGAAGAATTGAAATTGAAACACTGTAGAATTGATT
1 TTGAAGAATTGAAATTGAAACACTGTAGAATTGATT
* *
1567 TTGAAGAATTGAAATTGAAGCATTGTAGAATTGA
1 TTGAAGAATTGAAATTGAAACACTGTAGAATTGA
1601 AATTGAAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.41, C:0.04, G:0.21, T:0.33
Consensus pattern (36 bp):
TTGAAGAATTGAAATTGAAACACTGTAGAATTGATT
Found at i:1586 original size:14 final size:14
Alignment explanation
Indices: 1301--1549 Score: 103
Period size: 14 Copynumber: 17.4 Consensus size: 14
1291 AAATTTAAAC
1301 ATTGAAGAATTG-A
1 ATTGAAGAATTGAA
*
1314 ATCTGGAG-ATATGAA
1 AT-TGAAGAAT-TGAA
* *
1329 TTTGAAGCATTGAA
1 ATTGAAGAATTGAA
1343 ACGTTG-A-AATTGAAA
1 A--TTGAAGAATTG-AA
*
1358 CATTGAAGGATTGAA
1 -ATTGAAGAATTGAA
*
1373 TTTGAAGAATTGAA
1 ATTGAAGAATTGAA
*
1387 ATT-AAAACATTGAA
1 ATTGAAGA-ATTGAA
1401 GGATT--A-AATCTGGAGA
1 --ATTGAAGAAT-T-GA-A
1417 ATTG-A-AATTGAAA
1 ATTGAAGAATTG-AA
*
1430 CATTGAAGGATTGAA
1 -ATTGAAGAATTGAA
* *
1445 TTTGAGGAATTGAA
1 ATTGAAGAATTGAA
*
1459 ATTGAAGCATTGAAGA
1 ATTGAAGAATTG-A-A
1475 ATTG-A-AATTGAAGA
1 ATTGAAGAATTG-A-A
1489 ATTGAAGAATTGAA
1 ATTGAAGAATTGAA
* *
1503 ATTGAAGCATTGGA
1 ATTGAAGAATTGAA
*
1517 ATTG-A-AATTGAGG
1 ATTGAAGAATTGA-A
*
1530 CTTGAAGAATTGAA
1 ATTGAAGAATTGAA
1544 ATTGAA
1 ATTGAA
1550 ACACTGTAGA
Statistics
Matches: 182, Mismatches: 26, Indels: 55
0.69 0.10 0.21
Matches are distributed among these distances:
12 4 0.02
13 15 0.08
14 107 0.59
15 30 0.16
16 26 0.14
ACGTcount: A:0.43, C:0.04, G:0.23, T:0.29
Consensus pattern (14 bp):
ATTGAAGAATTGAA
Found at i:1607 original size:36 final size:37
Alignment explanation
Indices: 1414--1607 Score: 95
Period size: 36 Copynumber: 5.4 Consensus size: 37
1404 TTAAATCTGG
* * * *
1414 AGAATTGAAATTGAAACATTGAAGGATTGA-ATTTGA
1 AGAATTGAAATTGAAGCATTGTAGAATTGAGAATTGA
* *
1450 GGAATTGAAATTGAAGCATTGAAGAATTGA-AATTGA
1 AGAATTGAAATTGAAGCATTGTAGAATTGAGAATTGA
* *
1486 AGAATTGAAGAATTGAA--ATTGAAGCATTG-GAATTG-
1 AGAATTG-A-AATTGAAGCATTGTAGAATTGAGAATTGA
** * * * *
1521 A-AATTGAGGCTTGAAGAATTG-A-AATTGAAACACTGT
1 AGAATTGA-AATTGAAGCATTGTAGAATTGAGA-ATTGA
** * * *
1557 AGAATTGATTTTGAAGAATTG-A-AATTGAAGCATTGT
1 AGAATTGAAATTGAAGCATTGTAGAATTG-AGAATTGA
1593 AGAATTGAAATTGAA
1 AGAATTGAAATTGAA
1608 AAATTTTGAA
Statistics
Matches: 130, Mismatches: 18, Indels: 20
0.77 0.11 0.12
Matches are distributed among these distances:
33 11 0.08
34 7 0.05
35 8 0.06
36 89 0.68
37 8 0.06
38 7 0.05
ACGTcount: A:0.43, C:0.04, G:0.23, T:0.30
Consensus pattern (37 bp):
AGAATTGAAATTGAAGCATTGTAGAATTGAGAATTGA
Found at i:1732 original size:8 final size:8
Alignment explanation
Indices: 1697--1868 Score: 69
Period size: 8 Copynumber: 22.2 Consensus size: 8
1687 CATTGAAGTA
1697 AATTGAAG
1 AATTGAAG
*
1705 AATCGAAG
1 AATTGAAG
*
1713 CATTG-AG
1 AATTGAAG
1720 TAATTGAAG
1 -AATTGAAG
*
1729 AATTTAAG
1 AATTGAAG
1737 CAA-T-AAG
1 -AATTGAAG
* *
1744 TGATCGAAG
1 -AATTGAAG
1753 AATTGAAG
1 AATTGAAG
*
1761 AAAT--A-
1 AATTGAAG
1766 AATTGAAG
1 AATTGAAG
* *
1774 TATTGAAT
1 AATTGAAG
*
1782 AATTAAAG
1 AATTGAAG
* *
1790 AGTCGAAG
1 AATTGAAG
1798 -A--GATA-
1 AATTGA-AG
*
1803 AATTGAAT
1 AATTGAAG
*
1811 CATTGAAG
1 AATTGAAG
1819 AATTGAAG
1 AATTGAAG
1827 AATTGAA-
1 AATTGAAG
*
1834 TATTGGAAG
1 AATT-GAAG
*
1843 AGTTGAAG
1 AATTGAAG
* *
1851 CATTGAAT
1 AATTGAAG
1859 AATTGAAG
1 AATTGAAG
1867 AA
1 AA
1869 AGAGATCATT
Statistics
Matches: 117, Mismatches: 32, Indels: 30
0.65 0.18 0.17
Matches are distributed among these distances:
5 5 0.04
6 3 0.03
7 11 0.09
8 89 0.76
9 9 0.08
ACGTcount: A:0.47, C:0.04, G:0.22, T:0.27
Consensus pattern (8 bp):
AATTGAAG
Found at i:1737 original size:24 final size:24
Alignment explanation
Indices: 1687--1760 Score: 76
Period size: 24 Copynumber: 3.0 Consensus size: 24
1677 CACCTTGGGT
*
1687 CATTGAAGTAAATTGAAGAATCGAAG
1 CATTG-AGT-AATTGAAGAATTGAAG
*
1713 CATTGAGTAATTGAAGAATTTAAG
1 CATTGAGTAATTGAAGAATTGAAG
* * * *
1737 CAATAAGTGATCGAAGAATTGAAG
1 CATTGAGTAATTGAAGAATTGAAG
1761 AAATAAATTG
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
24 33 0.80
25 3 0.07
26 5 0.12
ACGTcount: A:0.45, C:0.07, G:0.23, T:0.26
Consensus pattern (24 bp):
CATTGAGTAATTGAAGAATTGAAG
Found at i:1798 original size:37 final size:37
Alignment explanation
Indices: 1757--1827 Score: 99
Period size: 37 Copynumber: 1.9 Consensus size: 37
1747 TCGAAGAATT
*
1757 GAAGAAATAAATTGAAGT-ATTGAATAATTAAAGAGTC
1 GAAGAAATAAATTGAA-TCATTGAAGAATTAAAGAGTC
* *
1794 GAAGAGATAAATTGAATCATTGAAGAATTGAAGA
1 GAAGAAATAAATTGAATCATTGAAGAATTAAAGA
1828 ATTGAATATT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
36 1 0.03
37 29 0.97
ACGTcount: A:0.51, C:0.03, G:0.21, T:0.25
Consensus pattern (37 bp):
GAAGAAATAAATTGAATCATTGAAGAATTAAAGAGTC
Found at i:1831 original size:24 final size:23
Alignment explanation
Indices: 1803--1868 Score: 87
Period size: 24 Copynumber: 2.7 Consensus size: 23
1793 CGAAGAGATA
1803 AATTGAATCATTGAAGAATTGAAG
1 AATTGAAT-ATTGAAGAATTGAAG
*
1827 AATTGAATATTGGAAGAGTTGAAG
1 AATTGAATATT-GAAGAATTGAAG
*
1851 CATTGAATAATTGAAGAA
1 AATTGAAT-ATTGAAGAA
1869 AGAGATCATT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
23 3 0.08
24 31 0.84
25 3 0.08
ACGTcount: A:0.45, C:0.03, G:0.23, T:0.29
Consensus pattern (23 bp):
AATTGAATATTGAAGAATTGAAG
Found at i:3593 original size:13 final size:13
Alignment explanation
Indices: 3577--3614 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
3567 ACGAGTTTCT
*
3577 AAAATTATTTTTG
1 AAAAATATTTTTG
*
3590 AAAAACATTTTTG
1 AAAAATATTTTTG
3603 AAAAATATTTTT
1 AAAAATATTTTT
3615 TTTTTGAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (13 bp):
AAAAATATTTTTG
Found at i:3711 original size:14 final size:14
Alignment explanation
Indices: 3687--3724 Score: 60
Period size: 13 Copynumber: 2.8 Consensus size: 14
3677 ACCATGACCC
*
3687 TTTTCTGAAAAACA
1 TTTTTTGAAAAACA
3701 -TTTTTGAAAAACA
1 TTTTTTGAAAAACA
3714 TTTTTTGAAAA
1 TTTTTTGAAAA
3725 TCATGACTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 12 0.55
14 10 0.45
ACGTcount: A:0.42, C:0.08, G:0.08, T:0.42
Consensus pattern (14 bp):
TTTTTTGAAAAACA
Found at i:3717 original size:12 final size:13
Alignment explanation
Indices: 3687--3724 Score: 58
Period size: 14 Copynumber: 2.8 Consensus size: 13
3677 ACCATGACCC
3687 TTTTCTGAAAAACA
1 TTTT-TGAAAAACA
3701 TTTTTGAAAAACA
1 TTTTTGAAAAACA
3714 TTTTTTGAAAA
1 -TTTTTGAAAA
3725 TCATGACTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 9 0.39
14 14 0.61
ACGTcount: A:0.42, C:0.08, G:0.08, T:0.42
Consensus pattern (13 bp):
TTTTTGAAAAACA
Done.