Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002428.1 Hibiscus syriacus cultivar Beakdansim tig00004966_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: 73780
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.34
Found at i:647 original size:20 final size:20
Alignment explanation
Indices: 624--702 Score: 54
Period size: 22 Copynumber: 3.8 Consensus size: 20
614 AATTCGCAAC
624 GCGATTTTGAAAAATGTGTT
1 GCGATTTTGAAAAATGTGTT
*
644 GCGATAGTT--AAAATGTGTTT
1 GCGAT-TTTGAAAAATGTG-TT
*
664 GCGAGAGTTTGAAAAACTGTTGTT
1 GC--GATTTTGAAAAA-TG-TGTT
**
688 GCGATAGTGAAAAAT
1 GCGATTTTGAAAAAT
703 CCAAAATAAG
Statistics
Matches: 45, Mismatches: 6, Indels: 15
0.68 0.09 0.23
Matches are distributed among these distances:
19 8 0.18
20 9 0.20
21 5 0.11
22 11 0.24
23 4 0.09
24 6 0.13
25 2 0.04
ACGTcount: A:0.33, C:0.06, G:0.27, T:0.34
Consensus pattern (20 bp):
GCGATTTTGAAAAATGTGTT
Found at i:698 original size:22 final size:20
Alignment explanation
Indices: 631--702 Score: 74
Period size: 24 Copynumber: 3.4 Consensus size: 20
621 AACGCGATTT
631 TGAAAAATGTGTTGCGATAG
1 TGAAAAATGTGTTGCGATAG
* *
651 T-TAAAATGTGTTTGCGAGAG
1 TGAAAAATGTG-TTGCGATAG
671 TTTGAAAAACTGTTGTTGCGATAG
1 --TGAAAAA-TG-TGTTGCGATAG
695 TGAAAAAT
1 TGAAAAAT
703 CCAAAATAAG
Statistics
Matches: 42, Mismatches: 4, Indels: 11
0.74 0.07 0.19
Matches are distributed among these distances:
19 8 0.19
20 9 0.21
21 1 0.02
22 8 0.19
23 4 0.10
24 10 0.24
25 2 0.05
ACGTcount: A:0.35, C:0.06, G:0.26, T:0.33
Consensus pattern (20 bp):
TGAAAAATGTGTTGCGATAG
Found at i:1127 original size:21 final size:21
Alignment explanation
Indices: 1103--1183 Score: 83
Period size: 21 Copynumber: 3.9 Consensus size: 21
1093 ATTTTAAAAA
1103 ATCGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTCGACT
* *
1124 ATCGCAACGTGAACTTGGACT
1 ATCGCAACGCGAACTTCGACT
* * * **
1145 ATCGCAA-ACGAATTTGGAAA
1 ATCGCAACGCGAACTTCGACT
*
1165 ATCACAACGCGAACTTCGA
1 ATCGCAACGCGAACTTCGA
1184 ACGTGAACTT
Statistics
Matches: 48, Mismatches: 11, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
20 14 0.29
21 34 0.71
ACGTcount: A:0.35, C:0.26, G:0.20, T:0.20
Consensus pattern (21 bp):
ATCGCAACGCGAACTTCGACT
Found at i:1276 original size:60 final size:60
Alignment explanation
Indices: 1100--1407 Score: 354
Period size: 60 Copynumber: 5.5 Consensus size: 60
1090 GCGATTTTAA
1100 AAAATCGCAACGCGAACTTCGACTATCGCAACGTGAACTTGGACTATCGCAAACGAATTTGG
1 AAAATCGCAACGCGAACTTCGACTATC-CAACGTGAACTTGGACTATCGC-AACGAATTTGG
*
1162 AAAATCACAACGCGAACTTCG-------AACGTGAACTTGGACTATCGCAACGAATTTGG
1 AAAATCGCAACGCGAACTTCGACTATCCAACGTGAACTTGGACTATCGCAACGAATTTGG
*
1215 AAAATCGCAATGCGAACTTCGACTATCCAACGTGAACTTGGACTATCGCAACGAATTTGG
1 AAAATCGCAACGCGAACTTCGACTATCCAACGTGAACTTGGACTATCGCAACGAATTTGG
*
1275 AAAATCGCAA--CGAACTTCG-------AACGTGAACTTGGACTATCGCAACGAATTTGA
1 AAAATCGCAACGCGAACTTCGACTATCCAACGTGAACTTGGACTATCGCAACGAATTTGG
* * * * *
1326 AAAATCGCAACTCGAACTTGGACTATCGCAA---GAATTTGGACTAACG-TA--AATTTGG
1 AAAATCGCAACGCGAACTTCGACTATC-CAACGTGAACTTGGACTATCGCAACGAATTTGG
*
1381 AAAATCGCAACGCGAACTTGGACTATC
1 AAAATCGCAACGCGAACTTCGACTATC
1408 GCAAAATCGC
Statistics
Matches: 219, Mismatches: 10, Indels: 41
0.81 0.04 0.15
Matches are distributed among these distances:
51 41 0.19
53 38 0.17
54 21 0.10
55 32 0.15
57 1 0.00
58 22 0.10
60 42 0.19
61 2 0.01
62 20 0.09
ACGTcount: A:0.35, C:0.22, G:0.20, T:0.22
Consensus pattern (60 bp):
AAAATCGCAACGCGAACTTCGACTATCCAACGTGAACTTGGACTATCGCAACGAATTTGG
Found at i:1310 original size:111 final size:112
Alignment explanation
Indices: 1099--1392 Score: 433
Period size: 111 Copynumber: 2.7 Consensus size: 112
1089 TGCGATTTTA
*
1099 AAAAATCGCAACGCGAACTTCGACTATCGCAACGTGAACTTGGACTATCGCAAACGAATTTGGAA
1 AAAAATCGCAATGCGAACTTCGACTATCGCAACGTGAACTTGGACTATCGC-AACGAATTTGGAA
*
1164 AATCACAACGCGAACTTCGAACGTGAACTTGGACTATCGCAACGAATTTG
65 AATCGCAA--CGAACTTCGAACGTGAACTTGGACTATCGCAACGAATTTG
*
1214 GAAAATCGCAATGCGAACTTCGACTATC-CAACGTGAACTTGGACTATCGCAACGAATTTGGAAA
1 AAAAATCGCAATGCGAACTTCGACTATCGCAACGTGAACTTGGACTATCGCAACGAATTTGGAAA
1278 ATCGCAACGAACTTCGAACGTGAACTTGGACTATCGCAACGAATTTG
66 ATCGCAACGAACTTCGAACGTGAACTTGGACTATCGCAACGAATTTG
* * * *
1325 AAAAATCGCAACT-CGAACTTGGACTATCGCAA---GAATTTGGACTAACG-TA--AATTTGGAA
1 AAAAATCGCAA-TGCGAACTTCGACTATCGCAACGTGAACTTGGACTATCGCAACGAATTTGGAA
1383 AATCGCAACG
65 AATCGCAACG
1393 CGAACTTGGA
Statistics
Matches: 169, Mismatches: 8, Indels: 13
0.89 0.04 0.07
Matches are distributed among these distances:
106 19 0.11
108 1 0.01
109 13 0.08
111 64 0.38
112 4 0.02
113 20 0.12
114 22 0.13
115 26 0.15
ACGTcount: A:0.36, C:0.22, G:0.20, T:0.22
Consensus pattern (112 bp):
AAAAATCGCAATGCGAACTTCGACTATCGCAACGTGAACTTGGACTATCGCAACGAATTTGGAAA
ATCGCAACGAACTTCGAACGTGAACTTGGACTATCGCAACGAATTTG
Found at i:1353 original size:21 final size:19
Alignment explanation
Indices: 1112--1411 Score: 139
Period size: 21 Copynumber: 16.0 Consensus size: 19
1102 AATCGCAACG
*
1112 CGAACTTCGACTATCGCAA
1 CGAACTTGGACTATCGCAA
1131 CGTGAACTTGGACTATCGCAAA
1 C--GAACTTGGACTATCGC-AA
* ** *
1153 CGAATTTGGAAAATCACAA
1 CGAACTTGGACTATCGCAA
*
1172 CG--C--GAACT-TCG-AA
1 CGAACTTGGACTATCGCAA
1185 CGTGAACTTGGACTATCGCAA
1 C--GAACTTGGACTATCGCAA
* **
1206 CGAATTTGGAAAATCGCAA
1 CGAACTTGGACTATCGCAA
*
1225 TGCGAACTTCGACTATC-CAA
1 --CGAACTTGGACTATCGCAA
1245 CGTGAACTTGGACTATCGCAA
1 C--GAACTTGGACTATCGCAA
* **
1266 CGAATTTGGAAAATCGCAA
1 CGAACTTGGACTATCGCAA
*
1285 CGAACTTCGA--A-CG---
1 CGAACTTGGACTATCGCAA
*
1298 TGAACTTGGACTATCGCAA
1 CGAACTTGGACTATCGCAA
* * **
1317 CGAATTTGAAAAATCGCAA
1 CGAACTTGGACTATCGCAA
1336 CTCGAACTTGGACTATCGCAA
1 --CGAACTTGGACTATCGCAA
* * *
1357 -GAATTTGGACTAACG-TA
1 CGAACTTGGACTATCGCAA
* **
1374 --AATTTGGAAAATCGCAA
1 CGAACTTGGACTATCGCAA
1391 CGCGAACTTGGACTATCGCAA
1 --CGAACTTGGACTATCGCAA
1412 AATCGCGTTG
Statistics
Matches: 207, Mismatches: 45, Indels: 56
0.67 0.15 0.18
Matches are distributed among these distances:
13 11 0.05
14 2 0.01
15 4 0.02
16 15 0.07
17 4 0.02
18 14 0.07
19 61 0.29
20 31 0.15
21 62 0.30
22 3 0.01
ACGTcount: A:0.35, C:0.22, G:0.20, T:0.22
Consensus pattern (19 bp):
CGAACTTGGACTATCGCAA
Found at i:1366 original size:18 final size:19
Alignment explanation
Indices: 1192--1411 Score: 111
Period size: 19 Copynumber: 11.7 Consensus size: 19
1182 GAACGTGAAC
1192 TTGGACTATCGCAACGAAT
1 TTGGACTATCGCAACGAAT
** *
1211 TTGGAAAATCGCAATGCGAAC
1 TTGGACTATCGCAA--CGAAT
* *
1232 TTCGACTATC-CAACGTGAAC
1 TTGGACTATCGCAAC--GAAT
1252 TTGGACTATCGCAACGAAT
1 TTGGACTATCGCAACGAAT
** *
1271 TTGGAAAATCGCAACGAAC
1 TTGGACTATCGCAACGAAT
* * *
1290 TTCGA--A-CG---TGAAC
1 TTGGACTATCGCAACGAAT
1303 TTGGACTATCGCAACGAAT
1 TTGGACTATCGCAACGAAT
* ** *
1322 TTGAAAAATCGCAACTCGAAC
1 TTGGACTATCGCAA--CGAAT
1343 TTGGACTATCGCAA-GAAT
1 TTGGACTATCGCAACGAAT
* *
1361 TTGGACTAACG-TA--AAT
1 TTGGACTATCGCAACGAAT
** *
1377 TTGGAAAATCGCAACGCGAAC
1 TTGGACTATCGCAA--CGAAT
1398 TTGGACTATCGCAA
1 TTGGACTATCGCAA
1412 AATCGCGTTG
Statistics
Matches: 150, Mismatches: 33, Indels: 34
0.69 0.15 0.16
Matches are distributed among these distances:
13 8 0.05
15 1 0.01
16 15 0.10
17 3 0.02
18 14 0.09
19 49 0.33
20 16 0.11
21 44 0.29
ACGTcount: A:0.35, C:0.21, G:0.20, T:0.23
Consensus pattern (19 bp):
TTGGACTATCGCAACGAAT
Found at i:6644 original size:33 final size:32
Alignment explanation
Indices: 6584--6645 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
6574 GATGAATTTT
* ** *
6584 TCGCAGAGGCAAGCTTGGGGGAGAAGAAGATA
1 TCGCAGAGGCAAACTACGGGGAAAAGAAGATA
6616 TCGCAGAGGCAAACTCACGGGGAAAAGAAG
1 TCGCAGAGGCAAACT-ACGGGGAAAAGAAG
6646 GGTATTTTAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
32 14 0.56
33 11 0.44
ACGTcount: A:0.37, C:0.16, G:0.37, T:0.10
Consensus pattern (32 bp):
TCGCAGAGGCAAACTACGGGGAAAAGAAGATA
Found at i:7462 original size:20 final size:20
Alignment explanation
Indices: 7437--7476 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
7427 ATCTCATATC
*
7437 GGATCTAGACGTTGCAATCA
1 GGATCTAGACGTTACAATCA
7457 GGATCTAGACGTTACAATCA
1 GGATCTAGACGTTACAATCA
7477 AGTATTACGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.20, G:0.23, T:0.25
Consensus pattern (20 bp):
GGATCTAGACGTTACAATCA
Found at i:12385 original size:22 final size:22
Alignment explanation
Indices: 12360--12430 Score: 70
Period size: 26 Copynumber: 3.0 Consensus size: 22
12350 ATAATCATTC
12360 AAACAAACCAAATATTCAAAAT
1 AAACAAACCAAATATTCAAAAT
* * *
12382 AAACAATCCAAACTAAATATCCAAAC
1 AAACAAACCAAA-T--AT-TCAAAAT
12408 AAACAAAGCCAAATATTCAAAAT
1 AAACAAA-CCAAATATTCAAAAT
12431 GTTTAAACAC
Statistics
Matches: 38, Mismatches: 6, Indels: 9
0.72 0.11 0.17
Matches are distributed among these distances:
22 11 0.29
23 6 0.16
24 2 0.05
25 2 0.05
26 12 0.32
27 5 0.13
ACGTcount: A:0.61, C:0.21, G:0.01, T:0.17
Consensus pattern (22 bp):
AAACAAACCAAATATTCAAAAT
Found at i:14207 original size:38 final size:38
Alignment explanation
Indices: 14153--14230 Score: 147
Period size: 38 Copynumber: 2.1 Consensus size: 38
14143 CCTTGAAAAG
14153 TTTCGGATTGACTGGAATGTAGTGATGATTGCAGGATT
1 TTTCGGATTGACTGGAATGTAGTGATGATTGCAGGATT
*
14191 TTTCGGATTGAGTGGAATGTAGTGATGATTGCAGGATT
1 TTTCGGATTGACTGGAATGTAGTGATGATTGCAGGATT
14229 TT
1 TT
14231 GTTGATGCAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.23, C:0.06, G:0.32, T:0.38
Consensus pattern (38 bp):
TTTCGGATTGACTGGAATGTAGTGATGATTGCAGGATT
Found at i:14523 original size:44 final size:44
Alignment explanation
Indices: 14411--14523 Score: 142
Period size: 44 Copynumber: 2.6 Consensus size: 44
14401 AGTGTATCGA
* * * **
14411 TGCACTGT-ATAGTGTATCGATGCACATTCAAGGAATGTATTGG
1 TGCACTGTCATAGTGTATCGATGCATATTCAAAGAATGCATCAG
14454 TGCATCT-TCATAGTGTATCGATGCATATTCAAA-AGATGCATCAG
1 TGCA-CTGTCATAGTGTATCGATGCATATTCAAAGA-ATGCATCAG
14498 TGCACTGTCATAGTGTATCGATGCAT
1 TGCACTGTCATAGTGTATCGATGCAT
14524 TGCGCATAAA
Statistics
Matches: 61, Mismatches: 5, Indels: 7
0.84 0.07 0.10
Matches are distributed among these distances:
43 8 0.13
44 53 0.87
ACGTcount: A:0.28, C:0.17, G:0.22, T:0.33
Consensus pattern (44 bp):
TGCACTGTCATAGTGTATCGATGCATATTCAAAGAATGCATCAG
Found at i:20223 original size:65 final size:64
Alignment explanation
Indices: 20154--20289 Score: 204
Period size: 65 Copynumber: 2.1 Consensus size: 64
20144 ACACTAATTA
*
20154 CATTCGATGTTTCAA-AAGAGCCAGGAGTGCATCGATGCATGGTCTGTGCATCGGTACAT-AAAA
1 CATTCGATGTTTCAATAA-AACCAGGAGTGCATCGATGCATGG-CTGTGCATCGGTAC-TCAAAA
*
20217 TG
63 TC
*
20219 CATTCGATGTTTCAATAAAATCAGGAGTGCATCGATGCATGGCTGTGCATCGGTACTCAAAATC
1 CATTCGATGTTTCAATAAAACCAGGAGTGCATCGATGCATGGCTGTGCATCGGTACTCAAAATC
20283 CATTCGA
1 CATTCGA
20290 ATTAGGGTGT
Statistics
Matches: 66, Mismatches: 3, Indels: 5
0.89 0.04 0.07
Matches are distributed among these distances:
63 1 0.02
64 26 0.39
65 37 0.56
66 2 0.03
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.27
Consensus pattern (64 bp):
CATTCGATGTTTCAATAAAACCAGGAGTGCATCGATGCATGGCTGTGCATCGGTACTCAAAATC
Found at i:26481 original size:23 final size:23
Alignment explanation
Indices: 26449--26514 Score: 107
Period size: 23 Copynumber: 2.9 Consensus size: 23
26439 GACATATATA
26449 TGGTCCTTCGGGACAATTCTACG
1 TGGTCCTTCGGGACAATTCTACG
* *
26472 TGGTCATTCGGGATAATTCTACG
1 TGGTCCTTCGGGACAATTCTACG
26495 TGGTCCTTCGGGAC-ATTCTA
1 TGGTCCTTCGGGACAATTCTA
26515 TATGGCACTC
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
22 6 0.15
23 33 0.85
ACGTcount: A:0.18, C:0.23, G:0.26, T:0.33
Consensus pattern (23 bp):
TGGTCCTTCGGGACAATTCTACG
Found at i:28687 original size:21 final size:22
Alignment explanation
Indices: 28646--28695 Score: 68
Period size: 21 Copynumber: 2.3 Consensus size: 22
28636 TTTCGGTATA
28646 ATTCTATGTGGTCCATTGGGAC
1 ATTCTATGTGGTCCATTGGGAC
*
28668 A-TCTATGTGGT-CTTTCGGGAC
1 ATTCTATGTGGTCCATT-GGGAC
28689 ATTCTAT
1 ATTCTAT
28696 ATGGCACTCG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
20 3 0.12
21 16 0.64
22 6 0.24
ACGTcount: A:0.18, C:0.18, G:0.24, T:0.40
Consensus pattern (22 bp):
ATTCTATGTGGTCCATTGGGAC
Found at i:29963 original size:109 final size:110
Alignment explanation
Indices: 29831--30055 Score: 276
Period size: 109 Copynumber: 2.1 Consensus size: 110
29821 ACGTTTTAAA
* * ** * * *
29831 TCCCCCAAACTTTGCCACATTTTTATAAAATGGTCACTGTCAGGGATTGTTTTTATAATTTTCCC
1 TCCCCCAAACTTTACCACATTTTTACAAAATAATCACTATCAGGGACTGTTTTCATAATTTTCCC
* *
29896 ATTTATATGTATG-TTTTTATTTTTTGG-AAAA-ATCTTACTCTAGG
66 ATTTACATGTATGCTTTGTATTTTTTGGTAAAATATCTT--TCTAGG
** * * *
29940 TCCCCCAAACTTTACCATGTTTTTGCAAATTAATCATTATCAGGGACTGTTTTCATAATTTTCCC
1 TCCCCCAAACTTTACCACATTTTTACAAAATAATCACTATCAGGGACTGTTTTCATAATTTTCCC
30005 ATTTACATGTATGCTTTGTATTTTTTGGTAAAATATCTTTCTAGG
66 ATTTACATGTATGCTTTGTATTTTTTGGTAAAATATCTTTCTAGG
*
30050 TTCCCC
1 TCCCCC
30056 TATGTTTTCC
Statistics
Matches: 98, Mismatches: 15, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
109 65 0.66
110 24 0.24
111 4 0.04
112 5 0.05
ACGTcount: A:0.25, C:0.19, G:0.12, T:0.44
Consensus pattern (110 bp):
TCCCCCAAACTTTACCACATTTTTACAAAATAATCACTATCAGGGACTGTTTTCATAATTTTCCC
ATTTACATGTATGCTTTGTATTTTTTGGTAAAATATCTTTCTAGG
Found at i:33885 original size:23 final size:23
Alignment explanation
Indices: 33855--33916 Score: 115
Period size: 23 Copynumber: 2.7 Consensus size: 23
33845 GGCAAGGACC
33855 TTTCAACAAATAAGCCCTTATAA
1 TTTCAACAAATAAGCCCTTATAA
*
33878 TTTCAACAAATAAGCCCTTCTAA
1 TTTCAACAAATAAGCCCTTATAA
33901 TTTCAACAAATAAGCC
1 TTTCAACAAATAAGCC
33917 TTAAATCTGC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.42, C:0.24, G:0.05, T:0.29
Consensus pattern (23 bp):
TTTCAACAAATAAGCCCTTATAA
Found at i:33950 original size:8 final size:8
Alignment explanation
Indices: 33934--34238 Score: 353
Period size: 8 Copynumber: 38.4 Consensus size: 8
33924 TGCAAGAATA
*
33934 TATGCATG
1 TATGTATG
33942 TATGTATG
1 TATGTATG
33950 TATGTATG
1 TATGTATG
33958 TATGTATG
1 TATGTATG
33966 TATGTATG
1 TATGTATG
33974 TATGTATG
1 TATGTATG
33982 TATGTATG
1 TATGTATG
33990 TATGTATG
1 TATGTATG
33998 TATGTATG
1 TATGTATG
34006 TATGTATG
1 TATGTATG
*
34014 TATATATG
1 TATGTATG
34022 TATGTATG
1 TATGTATG
34030 TATGTATG
1 TATGTATG
34038 TATGTATG
1 TATGTATG
34046 TATGTATG
1 TATGTATG
*
34054 TATGCATG
1 TATGTATG
* *
34062 CATGCATG
1 TATGTATG
*
34070 CATGTATG
1 TATGTATG
* *
34078 CATGCATG
1 TATGTATG
*
34086 CATGTA--
1 TATGTATG
34092 TATGTATG
1 TATGTATG
*
34100 TATGCATG
1 TATGTATG
*
34108 CATGTATG
1 TATGTATG
* *
34116 CATGCATG
1 TATGTATG
*
34124 CATGTATG
1 TATGTATG
*
34132 CATGTATG
1 TATGTATG
*
34140 CATGTATG
1 TATGTATG
*
34148 CATGTATG
1 TATGTATG
*
34156 CATGTATG
1 TATGTATG
*
34164 CATGTATG
1 TATGTATG
*
34172 CATGTATG
1 TATGTATG
*
34180 CATGTATG
1 TATGTATG
*
34188 CATGTATG
1 TATGTATG
*
34196 CATGTATG
1 TATGTATG
*
34204 CATGTATG
1 TATGTATG
*
34212 CATGTATG
1 TATGTATG
*
34220 TATGCATG
1 TATGTATG
*
34228 CATGTATG
1 TATGTATG
34236 TAT
1 TAT
34239 TCAATGATTC
Statistics
Matches: 276, Mismatches: 19, Indels: 4
0.92 0.06 0.01
Matches are distributed among these distances:
6 5 0.02
8 271 0.98
ACGTcount: A:0.26, C:0.09, G:0.24, T:0.42
Consensus pattern (8 bp):
TATGTATG
Found at i:33966 original size:24 final size:24
Alignment explanation
Indices: 33934--34238 Score: 394
Period size: 24 Copynumber: 12.6 Consensus size: 24
33924 TGCAAGAATA
33934 TATGCATGTATGTATGTATGTATG
1 TATGCATGTATGTATGTATGTATG
*
33958 TATGTATGTATGTATGTATGTATG
1 TATGCATGTATGTATGTATGTATG
*
33982 TATGTATGTATGTATGTATGTATG
1 TATGCATGTATGTATGTATGTATG
* *
34006 TATGTATGTATATATGTATGTATG
1 TATGCATGTATGTATGTATGTATG
*
34030 TATGTATGTATGTATGTATGTATG
1 TATGCATGTATGTATGTATGTATG
* * *
34054 TATGCATGCATGCATGCATGTATG
1 TATGCATGTATGTATGTATGTATG
* *
34078 CATGCATGCATGTATATGTATGTATG
1 TATGCATGTATG--TATGTATGTATG
* * * *
34104 CATGCATGTATGCATGCATGCATG
1 TATGCATGTATGTATGTATGTATG
* *
34128 TATGCATGTATGCATGTATGCATG
1 TATGCATGTATGTATGTATGTATG
* *
34152 TATGCATGTATGCATGTATGCATG
1 TATGCATGTATGTATGTATGTATG
* *
34176 TATGCATGTATGCATGTATGCATG
1 TATGCATGTATGTATGTATGTATG
*
34200 TATGCATGTATGCATGTATGTATG
1 TATGCATGTATGTATGTATGTATG
*
34224 CATGCATGTATGTAT
1 TATGCATGTATGTAT
34239 TCAATGATTC
Statistics
Matches: 260, Mismatches: 19, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
24 239 0.92
26 21 0.08
ACGTcount: A:0.26, C:0.09, G:0.24, T:0.42
Consensus pattern (24 bp):
TATGCATGTATGTATGTATGTATG
Found at i:34612 original size:39 final size:39
Alignment explanation
Indices: 34555--34632 Score: 113
Period size: 39 Copynumber: 2.0 Consensus size: 39
34545 ATAATCACTC
*
34555 TTATCAACCTATTTGATCTCA-ACTTGAACATAACATATT
1 TTATCAACCTATTCGATCT-ATACTTGAACATAACATATT
* *
34594 TTATCAACCTCTTCGATCTATTCTTGAACATAACATATT
1 TTATCAACCTATTCGATCTATACTTGAACATAACATATT
34633 ATTAACTTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
38 1 0.03
39 34 0.97
ACGTcount: A:0.33, C:0.22, G:0.05, T:0.40
Consensus pattern (39 bp):
TTATCAACCTATTCGATCTATACTTGAACATAACATATT
Found at i:39130 original size:21 final size:21
Alignment explanation
Indices: 39098--39137 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
39088 AACTACCCAG
39098 TATAGAGGGTATCGATACTCC
1 TATAGAGGGTATCGATACTCC
*
39119 TATAG-GGAGTATCGGTACT
1 TATAGAGG-GTATCGATACT
39138 ATCTTTGCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 2 0.12
21 15 0.88
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.30
Consensus pattern (21 bp):
TATAGAGGGTATCGATACTCC
Found at i:45837 original size:2 final size:2
Alignment explanation
Indices: 45830--45888 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
45820 TATCGATGAT
45830 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
45872 TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA T
45889 GATAATGTGT
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:47910 original size:8 final size:8
Alignment explanation
Indices: 47887--47937 Score: 54
Period size: 8 Copynumber: 6.5 Consensus size: 8
47877 TCAAAGTTTT
47887 GGTCAACAG
1 GGTCAAC-G
47896 TGGTCAACG
1 -GGTCAACG
*
47905 GGTCAACA
1 GGTCAACG
47913 GGTCAACG
1 GGTCAACG
47921 GGT---CG
1 GGTCAACG
47926 GGTCAACG
1 GGTCAACG
47934 GGTC
1 GGTC
47938 GGATCAACGG
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
5 5 0.14
8 23 0.64
9 1 0.03
10 7 0.19
ACGTcount: A:0.24, C:0.24, G:0.37, T:0.16
Consensus pattern (8 bp):
GGTCAACG
Found at i:47918 original size:16 final size:17
Alignment explanation
Indices: 47887--47924 Score: 60
Period size: 16 Copynumber: 2.2 Consensus size: 17
47877 TCAAAGTTTT
47887 GGTCAACAGTGGTCAACG
1 GGTCAACAG-GGTCAACG
47905 GGTCAACA-GGTCAACG
1 GGTCAACAGGGTCAACG
47921 GGTC
1 GGTC
47925 GGGTCAACGG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 12 0.60
18 8 0.40
ACGTcount: A:0.26, C:0.24, G:0.34, T:0.16
Consensus pattern (17 bp):
GGTCAACAGGGTCAACG
Found at i:47931 original size:13 final size:13
Alignment explanation
Indices: 47913--47986 Score: 76
Period size: 13 Copynumber: 5.3 Consensus size: 13
47903 CGGGTCAACA
47913 GGTCAACGGGTCG
1 GGTCAACGGGTCG
47926 GGTCAACGGGTCG
1 GGTCAACGGGTCG
*
47939 GATCAACGGGTCGAGTCG
1 GGTCAAC--G--G-GTCG
*
47957 GGTCAACTGGTCG
1 GGTCAACGGGTCG
*
47970 GGTAAACGGGTCG
1 GGTCAACGGGTCG
47983 GGTC
1 GGTC
47987 GGGTTATGAC
Statistics
Matches: 50, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
13 37 0.74
14 1 0.02
15 1 0.02
17 1 0.02
18 10 0.20
ACGTcount: A:0.18, C:0.22, G:0.43, T:0.18
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:47960 original size:31 final size:31
Alignment explanation
Indices: 47922--47990 Score: 102
Period size: 31 Copynumber: 2.2 Consensus size: 31
47912 AGGTCAACGG
*
47922 GTCGGGTCAACGGGTCGGATCAACGGGTCGA
1 GTCGGGTCAACGGGTCGGATAAACGGGTCGA
* * *
47953 GTCGGGTCAACTGGTCGGGTAAACGGGTCGG
1 GTCGGGTCAACGGGTCGGATAAACGGGTCGA
47984 GTCGGGT
1 GTCGGGT
47991 TATGACCGGT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.16, C:0.20, G:0.45, T:0.19
Consensus pattern (31 bp):
GTCGGGTCAACGGGTCGGATAAACGGGTCGA
Found at i:47962 original size:18 final size:18
Alignment explanation
Indices: 47935--47969 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
47925 GGGTCAACGG
47935 GTCGGATCAACGGGTCGA
1 GTCGGATCAACGGGTCGA
* *
47953 GTCGGGTCAACTGGTCG
1 GTCGGATCAACGGGTCG
47970 GGTAAACGGG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.17, C:0.23, G:0.40, T:0.20
Consensus pattern (18 bp):
GTCGGATCAACGGGTCGA
Found at i:49965 original size:35 final size:35
Alignment explanation
Indices: 49892--49966 Score: 114
Period size: 35 Copynumber: 2.1 Consensus size: 35
49882 CGTCACGTCC
**
49892 AGTAAGGCCCTGAACACACAGCCGAGGAACCGGTA
1 AGTAAGGCCCTGAACACACAGCCGAGGAACCGCCA
* *
49927 AGTAAGGCCCTGAGCACACAGCCGAGGAACCTCCA
1 AGTAAGGCCCTGAACACACAGCCGAGGAACCGCCA
49962 AGTAA
1 AGTAA
49967 TCTTCCTCCA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.35, C:0.29, G:0.27, T:0.09
Consensus pattern (35 bp):
AGTAAGGCCCTGAACACACAGCCGAGGAACCGCCA
Found at i:50071 original size:24 final size:24
Alignment explanation
Indices: 50044--50134 Score: 112
Period size: 24 Copynumber: 3.8 Consensus size: 24
50034 CATAATTCAA
*
50044 GTCAAGTATCATATCAGAATCCAG
1 GTCAAGTATCAGATCAGAATCCAG
* *
50068 GTCATGTATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAG
*
50092 GTCAA-TATCAGATCAGAATTCAG
1 GTCAAGTATCAGATCAGAATCCAG
* * *
50115 GTCAGGTATCATAACAGAAT
1 GTCAAGTATCAGATCAGAAT
50135 TCAAATTTGA
Statistics
Matches: 57, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
23 20 0.35
24 37 0.65
ACGTcount: A:0.37, C:0.19, G:0.18, T:0.26
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAG
Found at i:50116 original size:47 final size:48
Alignment explanation
Indices: 50044--50134 Score: 130
Period size: 47 Copynumber: 1.9 Consensus size: 48
50034 CATAATTCAA
* * *
50044 GTCAAGTATCATATCAGAATCCAGGTCATGTATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAGGTCAGGTATCAGAACAGAATCCAT
* *
50092 GTCAA-TATCAGATCAGAATTCAGGTCAGGTATCATAACAGAAT
1 GTCAAGTATCAGATCAGAATCCAGGTCAGGTATCAGAACAGAAT
50135 TCAAATTTGA
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
47 33 0.87
48 5 0.13
ACGTcount: A:0.37, C:0.19, G:0.18, T:0.26
Consensus pattern (48 bp):
GTCAAGTATCAGATCAGAATCCAGGTCAGGTATCAGAACAGAATCCAT
Found at i:52456 original size:16 final size:17
Alignment explanation
Indices: 52425--52462 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
52415 GGTCAACATT
*
52425 GGTCAACGTCGGTCAATG
1 GGTCAACG-CGGTCAACG
52443 GGTCAACG-GGTCAACG
1 GGTCAACGCGGTCAACG
52459 GGTC
1 GGTC
52463 GGTTCGGGTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 11 0.58
18 8 0.42
ACGTcount: A:0.21, C:0.24, G:0.37, T:0.18
Consensus pattern (17 bp):
GGTCAACGCGGTCAACG
Found at i:54420 original size:335 final size:334
Alignment explanation
Indices: 53811--54482 Score: 1263
Period size: 335 Copynumber: 2.0 Consensus size: 334
53801 GGAAGTCACA
* * *
53811 TTAGGGCCACCGGAGCGACCCACTATAAAAATAGCGGAAAATTTAAAACTTTTTTCAGAACATGT
1 TTAGGGCCACCGGAACGACCCACTATAAAAATAACGAAAAATTTAAAACTTTTTTCAGAACATGT
53876 AAACTTATAAAATCAGTTTTCACTATTTAAAAATAAAACAGATTTCCAAACTCGTATATAAATCA
66 AAACTTATAAAATCAGTTTTCACTATTTAAAAATAAAACAGATTTCCAAACTCGTATATAAATCA
53941 AAATACAATTACATGCCCCCTAATCACATGTACCATACTCTGCAACAACGCCGGACGAATTCCTT
131 AAATACAATTACATGCCCCCTAATCACATGTACCATACTCTGCAACAACGCCGGACGAATTCCTT
*
54006 TACTGATGTCGATAACTGCACTGGTATAATTCTTTTAACCTGAAAAGGTGAGTAATAGAGTGAGC
196 TACTGATGTCGATAACTGCACTGGTATAATTCTTTTAACCTGAAAAGGTAAGTAATAGAGTGAGC
54071 TTTAGAAAGCTCAGTAATACAGAACTACCAGATGATGCTGATGAACGTGCAGATACAGATAAACA
261 TTTAGAAAGCTCAGTAATACAGAACTACCAGATGATGCTGATGAACGTGCAGATACAGATAAACA
54136 TACATATCC
326 TACATATCC
*
54145 TTAGGGCCACCGGAACGACCCACTGTAAAAATAACGAAAAATTTAAAACTTTTTTTCAGAACATG
1 TTAGGGCCACCGGAACGACCCACTATAAAAATAACGAAAAATTTAAAAC-TTTTTTCAGAACATG
54210 TAAACTTATAAAATCAGTTTTCACTATTTAAAAATAAAACAGATTTCCAAACTCGTATATAAATC
65 TAAACTTATAAAATCAGTTTTCACTATTTAAAAATAAAACAGATTTCCAAACTCGTATATAAATC
54275 AAAATACAATTACATGCCCCCTAATCACATGTACCATACTCTGCAACAACGCCGGACGAATTCCT
130 AAAATACAATTACATGCCCCCTAATCACATGTACCATACTCTGCAACAACGCCGGACGAATTCCT
54340 TTACTGATGTCGATAACTGCACTGGTATAATTCTTTTAACCTGAAAAGGTAAGTAATAGAGTGAG
195 TTACTGATGTCGATAACTGCACTGGTATAATTCTTTTAACCTGAAAAGGTAAGTAATAGAGTGAG
* * *
54405 CTTTGGAAAGCTCAGTAATACAGAACTACCAGGTGATGCTGATGAACGTGTAGATACAGATAAAC
260 CTTTAGAAAGCTCAGTAATACAGAACTACCAGATGATGCTGATGAACGTGCAGATACAGATAAAC
54470 ATACATATCC
325 ATACATATCC
54480 TTA
1 TTA
54483 TTATTTCCGA
Statistics
Matches: 329, Mismatches: 8, Indels: 1
0.97 0.02 0.00
Matches are distributed among these distances:
334 45 0.14
335 284 0.86
ACGTcount: A:0.38, C:0.20, G:0.15, T:0.27
Consensus pattern (334 bp):
TTAGGGCCACCGGAACGACCCACTATAAAAATAACGAAAAATTTAAAACTTTTTTCAGAACATGT
AAACTTATAAAATCAGTTTTCACTATTTAAAAATAAAACAGATTTCCAAACTCGTATATAAATCA
AAATACAATTACATGCCCCCTAATCACATGTACCATACTCTGCAACAACGCCGGACGAATTCCTT
TACTGATGTCGATAACTGCACTGGTATAATTCTTTTAACCTGAAAAGGTAAGTAATAGAGTGAGC
TTTAGAAAGCTCAGTAATACAGAACTACCAGATGATGCTGATGAACGTGCAGATACAGATAAACA
TACATATCC
Found at i:54811 original size:35 final size:35
Alignment explanation
Indices: 54738--54812 Score: 105
Period size: 35 Copynumber: 2.1 Consensus size: 35
54728 CGTCACGTCC
* *
54738 AGTAAGGCACTGAGCACACAGCCGAGTAACCGATA
1 AGTAAGGCACTGAGCACACAGCCGAGGAACCGACA
* **
54773 AGTAAGGCCCTGAGCACACAGCCGAGGAACCTCCA
1 AGTAAGGCACTGAGCACACAGCCGAGGAACCGACA
54808 AGTAA
1 AGTAA
54813 TCTTCCTCCA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.36, C:0.28, G:0.25, T:0.11
Consensus pattern (35 bp):
AGTAAGGCACTGAGCACACAGCCGAGGAACCGACA
Found at i:54922 original size:24 final size:23
Alignment explanation
Indices: 54894--54980 Score: 102
Period size: 24 Copynumber: 3.7 Consensus size: 23
54884 ATTCAAGTTA
*
54894 AGTATCATATCAGAATCCAGGTC
1 AGTATCAGATCAGAATCCAGGTC
* *
54917 ATGTATCAGATCAGAATCTATGTC
1 A-GTATCAGATCAGAATCCAGGTC
*
54941 AATATCAGATCAGAATCCAGGTC
1 AGTATCAGATCAGAATCCAGGTC
* *
54964 AGGTATCATAACAGAAT
1 A-GTATCAGATCAGAAT
54981 TCAAATTTGA
Statistics
Matches: 53, Mismatches: 9, Indels: 3
0.82 0.14 0.05
Matches are distributed among these distances:
23 21 0.40
24 32 0.60
ACGTcount: A:0.38, C:0.18, G:0.17, T:0.26
Consensus pattern (23 bp):
AGTATCAGATCAGAATCCAGGTC
Found at i:54964 original size:23 final size:24
Alignment explanation
Indices: 54896--54964 Score: 95
Period size: 23 Copynumber: 2.9 Consensus size: 24
54886 TCAAGTTAAG
* *
54896 TATCATATCAGAATCCAGGTCATG
1 TATCAGATCAGAATCCAGGTCATA
* *
54920 TATCAGATCAGAATCTATGTCA-A
1 TATCAGATCAGAATCCAGGTCATA
54943 TATCAGATCAGAATCCAGGTCA
1 TATCAGATCAGAATCCAGGTCA
54965 GGTATCATAA
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
23 20 0.51
24 19 0.49
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.28
Consensus pattern (24 bp):
TATCAGATCAGAATCCAGGTCATA
Found at i:57266 original size:2 final size:2
Alignment explanation
Indices: 57261--57287 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
57251 TCAGATTTTG
57261 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
57288 AAGAGTTTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:59172 original size:10 final size:10
Alignment explanation
Indices: 59157--59188 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
59147 AAAAGTCATT
59157 GTTGCATATA
1 GTTGCATATA
59167 GTTGCATATA
1 GTTGCATATA
*
59177 GTTGCATTTA
1 GTTGCATATA
59187 GT
1 GT
59189 ACATTTATTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.25, C:0.09, G:0.22, T:0.44
Consensus pattern (10 bp):
GTTGCATATA
Found at i:60822 original size:19 final size:20
Alignment explanation
Indices: 60785--60822 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
60775 CACTCACTAC
**
60785 TGTATTACTTGCATTGATTG
1 TGTATTACTTGCACAGATTG
60805 TGTA-TACTTGCACAGATT
1 TGTATTACTTGCACAGATT
60823 TACGTGTCAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 12 0.75
20 4 0.25
ACGTcount: A:0.24, C:0.13, G:0.18, T:0.45
Consensus pattern (20 bp):
TGTATTACTTGCACAGATTG
Found at i:63714 original size:2 final size:2
Alignment explanation
Indices: 63707--63775 Score: 138
Period size: 2 Copynumber: 34.5 Consensus size: 2
63697 GTTTCATCAG
63707 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
63749 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
63776 TATGTTTTTG
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 67 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:65391 original size:28 final size:28
Alignment explanation
Indices: 65349--65407 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 28
65339 TAATCTAGGG
* *
65349 TAAGTACAAGACAATATTTGTTCAAAGA
1 TAAGTAAAAGACAATATATGTTCAAAGA
* *
65377 TAAGTAAAAGGCAATATATGTTTAAAGA
1 TAAGTAAAAGACAATATATGTTCAAAGA
65405 TAA
1 TAA
65408 CTCTCAATCA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.49, C:0.07, G:0.15, T:0.29
Consensus pattern (28 bp):
TAAGTAAAAGACAATATATGTTCAAAGA
Done.