Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006856.1 Hibiscus syriacus cultivar Beakdansim tig00017446_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: 1184065
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
File 4 of 4
Found at i:1082625 original size:22 final size:21
Alignment explanation
Indices: 1082599--1082639 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
1082589 GTTGTGGAAT
1082599 TGATGGTCTTGATGGATGAAGA
1 TGATGGTCTTGAT-GATGAAGA
*
1082621 TGATGGTGTTGATGATGAA
1 TGATGGTCTTGATGATGAA
1082640 ATGGAGATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.27, C:0.02, G:0.37, T:0.34
Consensus pattern (21 bp):
TGATGGTCTTGATGATGAAGA
Found at i:1087840 original size:10 final size:9
Alignment explanation
Indices: 1087824--1087884 Score: 52
Period size: 11 Copynumber: 6.2 Consensus size: 9
1087814 TTTAAATTTC
1087824 TTTTTCTTT
1 TTTTTCTTT
1087833 TCTTTTC-TT
1 T-TTTTCTTT
1087842 TTTTTCTGATT
1 TTTTTCT--TT
1087853 TTTTTCTGATT
1 TTTTTCT--TT
*
1087864 TTTGTCTTT
1 TTTTTCTTT
1087873 TCTTTTCTTT
1 T-TTTTCTTT
1087883 TT
1 TT
1087885 GCACTCCAAT
Statistics
Matches: 45, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
8 5 0.11
9 8 0.18
10 13 0.29
11 19 0.42
ACGTcount: A:0.03, C:0.13, G:0.05, T:0.79
Consensus pattern (9 bp):
TTTTTCTTT
Found at i:1087854 original size:11 final size:11
Alignment explanation
Indices: 1087840--1087866 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
1087830 TTTTCTTTTC
1087840 TTTTTTTCTGA
1 TTTTTTTCTGA
1087851 TTTTTTTCTGA
1 TTTTTTTCTGA
1087862 TTTTT
1 TTTTT
1087867 GTCTTTTCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.07, C:0.07, G:0.07, T:0.78
Consensus pattern (11 bp):
TTTTTTTCTGA
Found at i:1088225 original size:22 final size:21
Alignment explanation
Indices: 1088199--1088239 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
1088189 GCTGCGGAAT
1088199 TGATGGTCTTGATGGATGAAGA
1 TGATGGTCTTGAT-GATGAAGA
*
1088221 TGATGGTGTTGATGATGAA
1 TGATGGTCTTGATGATGAA
1088240 ATAGAGATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.27, C:0.02, G:0.37, T:0.34
Consensus pattern (21 bp):
TGATGGTCTTGATGATGAAGA
Found at i:1090117 original size:19 final size:19
Alignment explanation
Indices: 1090093--1090134 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
1090083 TAGTGTTCCA
*
1090093 TGAGCTGCCTTGTACTTTG
1 TGAGCTGCCCTGTACTTTG
1090112 TGAGCTGCCCTGTACTTTG
1 TGAGCTGCCCTGTACTTTG
1090131 TGAG
1 TGAG
1090135 ATGCATATGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.12, C:0.21, G:0.29, T:0.38
Consensus pattern (19 bp):
TGAGCTGCCCTGTACTTTG
Found at i:1098862 original size:23 final size:23
Alignment explanation
Indices: 1098834--1098937 Score: 65
Period size: 23 Copynumber: 4.4 Consensus size: 23
1098824 ACAAATTTTC
1098834 CATCACCATTATCA-CGCCTATAT
1 CATCACCATTATCATCGCC-ATAT
*
1098857 CATCACCA-TAGTCCATCTCCAT-T
1 CATCACCATTA-T-CATCGCCATAT
* *
1098880 -ATCACGCCTATATCATCACCATAGT
1 CATCAC-CAT-TATCATCGCCATA-T
*
1098905 CCATCACCATTATCA-CGCCTTTAT
1 -CATCACCATTATCATCGCC-ATAT
1098929 CATCACCAT
1 CATCACCAT
1098938 AGTCCATCTC
Statistics
Matches: 64, Mismatches: 6, Indels: 22
0.70 0.07 0.24
Matches are distributed among these distances:
22 7 0.11
23 28 0.44
24 9 0.14
25 13 0.20
26 2 0.03
27 5 0.08
ACGTcount: A:0.29, C:0.37, G:0.05, T:0.30
Consensus pattern (23 bp):
CATCACCATTATCATCGCCATAT
Found at i:1098879 original size:36 final size:36
Alignment explanation
Indices: 1098832--1099008 Score: 282
Period size: 36 Copynumber: 4.9 Consensus size: 36
1098822 ATACAAATTT
1098832 TCCATCACCATTATCACGCCTATATCATCACCATAG
1 TCCATCACCATTATCACGCCTATATCATCACCATAG
*
1098868 TCCATCTCCATTATCACGCCTATATCATCACCATAG
1 TCCATCACCATTATCACGCCTATATCATCACCATAG
*
1098904 TCCATCACCATTATCACGCCTTTATCATCACCATAG
1 TCCATCACCATTATCACGCCTATATCATCACCATAG
* * *
1098940 TCCATCTCCATTATCACGCCTATATCGTCACCATAT
1 TCCATCACCATTATCACGCCTATATCATCACCATAG
* * *
1098976 TCCACCACCATTATCACGCCCATATTATCACCA
1 TCCATCACCATTATCACGCCTATATCATCACCA
1099009 ACTTATAAAT
Statistics
Matches: 129, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 129 1.00
ACGTcount: A:0.28, C:0.37, G:0.05, T:0.29
Consensus pattern (36 bp):
TCCATCACCATTATCACGCCTATATCATCACCATAG
Found at i:1098911 original size:13 final size:11
Alignment explanation
Indices: 1098834--1098975 Score: 58
Period size: 11 Copynumber: 12.0 Consensus size: 11
1098824 ACAAATTTTC
1098834 CATCACCATTAT
1 CATCACCA-TAT
*
1098846 CA-CGCCTATAT
1 CATCACC-ATAT
1098857 CATCACCATAGT
1 CATCACCATA-T
*
1098869 CCATCTCCATTAT
1 -CATCACCA-TAT
*
1098882 CA-CGCCTATAT
1 CATCACC-ATAT
1098893 CATCACCATAGT
1 CATCACCATA-T
1098905 CCATCACCATTAT
1 -CATCACCA-TAT
* *
1098918 CA-CGCCTTTAT
1 CATCACC-ATAT
1098929 CATCACCATAGT
1 CATCACCATA-T
*
1098941 CCATCTCCATTAT
1 -CATCACCA-TAT
*
1098954 CA-CGCCTATAT
1 CATCACC-ATAT
*
1098965 CGTCACCATAT
1 CATCACCATAT
1098976 TCCACCACCA
Statistics
Matches: 100, Mismatches: 13, Indels: 35
0.68 0.09 0.24
Matches are distributed among these distances:
11 43 0.43
12 26 0.26
13 25 0.25
14 6 0.06
ACGTcount: A:0.28, C:0.36, G:0.06, T:0.30
Consensus pattern (11 bp):
CATCACCATAT
Found at i:1103462 original size:36 final size:36
Alignment explanation
Indices: 1103415--1103523 Score: 191
Period size: 36 Copynumber: 3.0 Consensus size: 36
1103405 ATACAAATTT
1103415 TCCATCACCATTATCACGCCTATATCATCACCATAG
1 TCCATCACCATTATCACGCCTATATCATCACCATAG
*
1103451 TCCATCTCCATTATCACGCCTATATCATCACCATAG
1 TCCATCACCATTATCACGCCTATATCATCACCATAG
* *
1103487 TCCATCACCATTATCACGCCTTTATCATCTCCATAG
1 TCCATCACCATTATCACGCCTATATCATCACCATAG
1103523 T
1 T
1103524 GATGTGAGTT
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 69 1.00
ACGTcount: A:0.28, C:0.36, G:0.06, T:0.31
Consensus pattern (36 bp):
TCCATCACCATTATCACGCCTATATCATCACCATAG
Found at i:1103494 original size:13 final size:11
Alignment explanation
Indices: 1103417--1103502 Score: 50
Period size: 11 Copynumber: 7.2 Consensus size: 11
1103407 ACAAATTTTC
1103417 CATCACCATTAT
1 CATCACCA-TAT
*
1103429 CA-CGCCTATAT
1 CATCACC-ATAT
1103440 CATCACCATAGT
1 CATCACCATA-T
*
1103452 CCATCTCCATTAT
1 -CATCACCA-TAT
*
1103465 CA-CGCCTATAT
1 CATCACC-ATAT
1103476 CATCACCATAGT
1 CATCACCATA-T
1103488 CCATCACCATTAT
1 -CATCACCA-TAT
1103501 CA
1 CA
1103503 CGCCTTTATC
Statistics
Matches: 59, Mismatches: 5, Indels: 20
0.70 0.06 0.24
Matches are distributed among these distances:
11 22 0.37
12 16 0.27
13 17 0.29
14 4 0.07
ACGTcount: A:0.30, C:0.36, G:0.05, T:0.29
Consensus pattern (11 bp):
CATCACCATAT
Found at i:1104919 original size:13 final size:11
Alignment explanation
Indices: 1104842--1104927 Score: 50
Period size: 11 Copynumber: 7.2 Consensus size: 11
1104832 ACAAATTTTC
1104842 CATCACCATTAT
1 CATCACCA-TAT
*
1104854 CA-CGCCTATAT
1 CATCACC-ATAT
1104865 CATCACCATAGT
1 CATCACCATA-T
*
1104877 CCATCTCCATTAT
1 -CATCACCA-TAT
*
1104890 CA-CGCCTATAT
1 CATCACC-ATAT
1104901 CATCACCATAGT
1 CATCACCATA-T
1104913 CCATCACCATTAT
1 -CATCACCA-TAT
1104926 CA
1 CA
1104928 CGCCTTTATC
Statistics
Matches: 59, Mismatches: 5, Indels: 20
0.70 0.06 0.24
Matches are distributed among these distances:
11 22 0.37
12 16 0.27
13 17 0.29
14 4 0.07
ACGTcount: A:0.30, C:0.36, G:0.05, T:0.29
Consensus pattern (11 bp):
CATCACCATAT
Found at i:1104948 original size:36 final size:36
Alignment explanation
Indices: 1104840--1104940 Score: 184
Period size: 36 Copynumber: 2.8 Consensus size: 36
1104830 ATACAAATTT
1104840 TCCATCACCATTATCACGCCTATATCATCACCATAG
1 TCCATCACCATTATCACGCCTATATCATCACCATAG
*
1104876 TCCATCTCCATTATCACGCCTATATCATCACCATAG
1 TCCATCACCATTATCACGCCTATATCATCACCATAG
*
1104912 TCCATCACCATTATCACGCCTTTATCATC
1 TCCATCACCATTATCACGCCTATATCATC
1104941 TCTATAGTGA
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 62 1.00
ACGTcount: A:0.28, C:0.37, G:0.05, T:0.31
Consensus pattern (36 bp):
TCCATCACCATTATCACGCCTATATCATCACCATAG
Found at i:1106344 original size:13 final size:11
Alignment explanation
Indices: 1106267--1106352 Score: 50
Period size: 11 Copynumber: 7.2 Consensus size: 11
1106257 ACAAATTTTC
1106267 CATCACCATTAT
1 CATCACCA-TAT
*
1106279 CA-CGCCTATAT
1 CATCACC-ATAT
1106290 CATCACCATAGT
1 CATCACCATA-T
*
1106302 CCATCTCCATTAT
1 -CATCACCA-TAT
*
1106315 CA-CGCCTATAT
1 CATCACC-ATAT
1106326 CATCACCATAGT
1 CATCACCATA-T
1106338 CCATCACCATTAT
1 -CATCACCA-TAT
1106351 CA
1 CA
1106353 CGCCTTTATC
Statistics
Matches: 59, Mismatches: 5, Indels: 20
0.70 0.06 0.24
Matches are distributed among these distances:
11 22 0.37
12 16 0.27
13 17 0.29
14 4 0.07
ACGTcount: A:0.30, C:0.36, G:0.05, T:0.29
Consensus pattern (11 bp):
CATCACCATAT
Found at i:1106373 original size:36 final size:36
Alignment explanation
Indices: 1106265--1106365 Score: 184
Period size: 36 Copynumber: 2.8 Consensus size: 36
1106255 ATACAAATTT
1106265 TCCATCACCATTATCACGCCTATATCATCACCATAG
1 TCCATCACCATTATCACGCCTATATCATCACCATAG
*
1106301 TCCATCTCCATTATCACGCCTATATCATCACCATAG
1 TCCATCACCATTATCACGCCTATATCATCACCATAG
*
1106337 TCCATCACCATTATCACGCCTTTATCATC
1 TCCATCACCATTATCACGCCTATATCATC
1106366 TCTATAGTGA
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 62 1.00
ACGTcount: A:0.28, C:0.37, G:0.05, T:0.31
Consensus pattern (36 bp):
TCCATCACCATTATCACGCCTATATCATCACCATAG
Found at i:1107767 original size:33 final size:33
Alignment explanation
Indices: 1107688--1107791 Score: 95
Period size: 33 Copynumber: 3.1 Consensus size: 33
1107678 ATACAATCTG
* *
1107688 TCCATCACCATTATCACGCCTATATCATCA-CCATAT
1 TCCATCACCA-TATCACGCCAATAACATCATCC---T
1107724 TCCATCACCATATCACGCCAATAACATCATCCT
1 TCCATCACCATATCACGCCAATAACATCATCCT
* * * *
1107757 TCCATTACCATTTCATCACCATTAA-ATCATCCT
1 TCCATCACCATATCA-CGCCAATAACATCATCCT
1107790 TC
1 TC
1107792 ATTCATCAAC
Statistics
Matches: 60, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
33 24 0.40
34 7 0.12
35 17 0.28
36 12 0.20
ACGTcount: A:0.31, C:0.37, G:0.02, T:0.31
Consensus pattern (33 bp):
TCCATCACCATATCACGCCAATAACATCATCCT
Found at i:1113444 original size:33 final size:33
Alignment explanation
Indices: 1113365--1113468 Score: 95
Period size: 33 Copynumber: 3.1 Consensus size: 33
1113355 ATACAATCTG
* *
1113365 TCCATCACCATTATCACGCCTATATCATCA-CCATAT
1 TCCATCACCA-TATCACGCCAATAACATCATCC---T
1113401 TCCATCACCATATCACGCCAATAACATCATCCT
1 TCCATCACCATATCACGCCAATAACATCATCCT
* * * *
1113434 TCCATTACCATTTCATCACCATTAA-ATCATCCT
1 TCCATCACCATATCA-CGCCAATAACATCATCCT
1113467 TC
1 TC
1113469 ATTCATCAAC
Statistics
Matches: 60, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
33 24 0.40
34 7 0.12
35 17 0.28
36 12 0.20
ACGTcount: A:0.31, C:0.37, G:0.02, T:0.31
Consensus pattern (33 bp):
TCCATCACCATATCACGCCAATAACATCATCCT
Found at i:1123846 original size:21 final size:21
Alignment explanation
Indices: 1123820--1123861 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
1123810 GTGACCTTTC
1123820 ATAAATAGTTGCTGCCCCATT
1 ATAAATAGTTGCTGCCCCATT
1123841 ATAAATAGTTGCTGCCCCATT
1 ATAAATAGTTGCTGCCCCATT
1123862 GATGCCATGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.29, C:0.24, G:0.14, T:0.33
Consensus pattern (21 bp):
ATAAATAGTTGCTGCCCCATT
Found at i:1124520 original size:13 final size:11
Alignment explanation
Indices: 1124478--1124563 Score: 68
Period size: 11 Copynumber: 7.3 Consensus size: 11
1124468 ATACAATCTT
1124478 TCATCACCATTA
1 TCATCACCA-TA
*
1124490 TCA-CACCTAAA
1 TCATCACC-ATA
1124501 TCATCACCATA
1 TCATCACCATA
1124512 GTCCATCACCATTA
1 -T-CATCACCA-TA
*
1124526 TCA-CGCCTATA
1 TCATCACC-ATA
1124537 TCATCACCATA
1 TCATCACCATA
1124548 TTCCATCACCATA
1 -T-CATCACCATA
1124561 TCA
1 TCA
1124564 CGCCTATATT
Statistics
Matches: 61, Mismatches: 4, Indels: 19
0.73 0.05 0.23
Matches are distributed among these distances:
11 23 0.38
12 17 0.28
13 19 0.31
14 2 0.03
ACGTcount: A:0.34, C:0.36, G:0.02, T:0.28
Consensus pattern (11 bp):
TCATCACCATA
Found at i:1124526 original size:36 final size:36
Alignment explanation
Indices: 1124479--1124580 Score: 161
Period size: 36 Copynumber: 2.9 Consensus size: 36
1124469 TACAATCTTT
* *
1124479 CATCACCATTATCACACCTAAATCATCACCATAGTC
1 CATCACCATTATCACGCCTATATCATCACCATAGTC
*
1124515 CATCACCATTATCACGCCTATATCATCACCATATTC
1 CATCACCATTATCACGCCTATATCATCACCATAGTC
*
1124551 CATCACCA-TATCACGCCTATATTATCACCA
1 CATCACCATTATCACGCCTATATCATCACCA
1124581 ACTTCTAAAT
Statistics
Matches: 62, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
35 21 0.34
36 41 0.66
ACGTcount: A:0.33, C:0.36, G:0.03, T:0.27
Consensus pattern (36 bp):
CATCACCATTATCACGCCTATATCATCACCATAGTC
Found at i:1134631 original size:21 final size:21
Alignment explanation
Indices: 1134605--1134646 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
1134595 GTGACCTTTC
1134605 ATAAATAGTTGCTGCCCCATT
1 ATAAATAGTTGCTGCCCCATT
1134626 ATAAATAGTTGCTGCCCCATT
1 ATAAATAGTTGCTGCCCCATT
1134647 GATGCCATGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.29, C:0.24, G:0.14, T:0.33
Consensus pattern (21 bp):
ATAAATAGTTGCTGCCCCATT
Found at i:1135308 original size:13 final size:11
Alignment explanation
Indices: 1135288--1135351 Score: 58
Period size: 13 Copynumber: 5.4 Consensus size: 11
1135278 TCACGCCTAA
1135288 ATCATCACCAT
1 ATCATCACCAT
1135299 AGTCCATCACCATT
1 A-T-CATCACCA-T
*
1135313 ATCA-CGCCTAT
1 ATCATCACC-AT
1135324 ATCATCACCAT
1 ATCATCACCAT
1135335 ATTCCATCACCAT
1 A-T-CATCACCAT
1135348 ATCA
1 ATCA
1135352 CGCCTATATT
Statistics
Matches: 44, Mismatches: 2, Indels: 14
0.73 0.03 0.23
Matches are distributed among these distances:
11 14 0.32
12 9 0.20
13 19 0.43
14 2 0.05
ACGTcount: A:0.33, C:0.36, G:0.03, T:0.28
Consensus pattern (11 bp):
ATCATCACCAT
Found at i:1135312 original size:36 final size:36
Alignment explanation
Indices: 1135265--1135368 Score: 174
Period size: 36 Copynumber: 2.9 Consensus size: 36
1135255 GATACAATCT
*
1135265 TCCATCACCATTATCACGCCTAAATCATCACCATAG
1 TCCATCACCATTATCACGCCTATATCATCACCATAG
*
1135301 TCCATCACCATTATCACGCCTATATCATCACCATAT
1 TCCATCACCATTATCACGCCTATATCATCACCATAG
*
1135337 TCCATCACCA-TATCACGCCTATATTATCACCA
1 TCCATCACCATTATCACGCCTATATCATCACCA
1135369 ACTTCTAAAT
Statistics
Matches: 65, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
35 21 0.32
36 44 0.68
ACGTcount: A:0.32, C:0.37, G:0.04, T:0.28
Consensus pattern (36 bp):
TCCATCACCATTATCACGCCTATATCATCACCATAG
Found at i:1138491 original size:12 final size:12
Alignment explanation
Indices: 1138474--1138501 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
1138464 TCTACCCATA
1138474 CTTTTAAAAGAG
1 CTTTTAAAAGAG
1138486 CTTTTAAAAGAG
1 CTTTTAAAAGAG
1138498 CTTT
1 CTTT
1138502 ATCTTGTATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.36, C:0.11, G:0.14, T:0.39
Consensus pattern (12 bp):
CTTTTAAAAGAG
Found at i:1141390 original size:21 final size:21
Alignment explanation
Indices: 1141364--1141405 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
1141354 GTGACCTTTC
1141364 ATAAATAGTTGCTGCCCCATT
1 ATAAATAGTTGCTGCCCCATT
1141385 ATAAATAGTTGCTGCCCCATT
1 ATAAATAGTTGCTGCCCCATT
1141406 GATGCCATGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.29, C:0.24, G:0.14, T:0.33
Consensus pattern (21 bp):
ATAAATAGTTGCTGCCCCATT
Found at i:1142067 original size:13 final size:11
Alignment explanation
Indices: 1142047--1142110 Score: 58
Period size: 13 Copynumber: 5.4 Consensus size: 11
1142037 TCACGCCTAA
1142047 ATCATCACCAT
1 ATCATCACCAT
1142058 AGTCCATCACCATT
1 A-T-CATCACCA-T
*
1142072 ATCA-CGCCTAT
1 ATCATCACC-AT
1142083 ATCATCACCAT
1 ATCATCACCAT
1142094 ATTCCATCACCAT
1 A-T-CATCACCAT
1142107 ATCA
1 ATCA
1142111 CGCCTATATT
Statistics
Matches: 44, Mismatches: 2, Indels: 14
0.73 0.03 0.23
Matches are distributed among these distances:
11 14 0.32
12 9 0.20
13 19 0.43
14 2 0.05
ACGTcount: A:0.33, C:0.36, G:0.03, T:0.28
Consensus pattern (11 bp):
ATCATCACCAT
Found at i:1142071 original size:36 final size:36
Alignment explanation
Indices: 1142024--1142127 Score: 174
Period size: 36 Copynumber: 2.9 Consensus size: 36
1142014 GATACAATCT
*
1142024 TCCATCACCATTATCACGCCTAAATCATCACCATAG
1 TCCATCACCATTATCACGCCTATATCATCACCATAG
*
1142060 TCCATCACCATTATCACGCCTATATCATCACCATAT
1 TCCATCACCATTATCACGCCTATATCATCACCATAG
*
1142096 TCCATCACCA-TATCACGCCTATATTATCACCA
1 TCCATCACCATTATCACGCCTATATCATCACCA
1142128 ACTTCTAAAT
Statistics
Matches: 65, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
35 21 0.32
36 44 0.68
ACGTcount: A:0.32, C:0.37, G:0.04, T:0.28
Consensus pattern (36 bp):
TCCATCACCATTATCACGCCTATATCATCACCATAG
Found at i:1147196 original size:6 final size:6
Alignment explanation
Indices: 1147185--1147228 Score: 54
Period size: 6 Copynumber: 7.2 Consensus size: 6
1147175 GATGTAGGAG
*
1147185 TCTTTT TC-TTT TCTTTT TATTTT TCTTCTT TCTTTT TCTCTTT T
1 TCTTTT TCTTTT TCTTTT TCTTTT TCTT-TT TCTTTT TCT-TTT T
1147229 TGTTGCTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
5 5 0.15
6 18 0.55
7 10 0.30
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (6 bp):
TCTTTT
Found at i:1147457 original size:15 final size:15
Alignment explanation
Indices: 1147439--1147481 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 15
1147429 TTAAGAAAGG
1147439 AAATGGAAAGAATTA
1 AAATGGAAAGAATTA
* *
1147454 AAATGGAAAGTATTG
1 AAATGGAAAGAATTA
*
1147469 AAATGGATAGAAT
1 AAATGGAAAGAAT
1147482 AGTTATCAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.53, C:0.00, G:0.23, T:0.23
Consensus pattern (15 bp):
AAATGGAAAGAATTA
Found at i:1155323 original size:33 final size:33
Alignment explanation
Indices: 1155281--1155349 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
1155271 GTTGATGAAT
*
1155281 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
1155314 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
1155347 GAA
1 GAA
1155350 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:1157303 original size:16 final size:16
Alignment explanation
Indices: 1157282--1157314 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
1157272 TTCTGCCACC
1157282 TATGTTAGAATGCAAA
1 TATGTTAGAATGCAAA
*
1157298 TATGTTAGGATGCAAA
1 TATGTTAGAATGCAAA
1157314 T
1 T
1157315 GAGCTAACTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.39, C:0.06, G:0.21, T:0.33
Consensus pattern (16 bp):
TATGTTAGAATGCAAA
Found at i:1162564 original size:11 final size:13
Alignment explanation
Indices: 1162532--1162561 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1162522 TGGCCAAAGA
1162532 TGAAAAGGTATGT
1 TGAAAAGGTATGT
1162545 TGAAAAGGTATG-
1 TGAAAAGGTATGT
1162557 TGAAA
1 TGAAA
1162562 GGTGTTTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.27
Consensus pattern (13 bp):
TGAAAAGGTATGT
Found at i:1165370 original size:23 final size:23
Alignment explanation
Indices: 1165317--1165371 Score: 60
Period size: 23 Copynumber: 2.3 Consensus size: 23
1165307 AGATGTAATA
*
1165317 TATGTATATGAATATAACTATGT
1 TATGTATATGAATATAACTATAT
1165340 TATAGTATATGAA-ATAAGC-ATCAT
1 TAT-GTATATGAATATAA-CTAT-AT
1165364 TATGTATA
1 TATGTATA
1165372 AATATAGAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
23 14 0.50
24 14 0.50
ACGTcount: A:0.42, C:0.05, G:0.13, T:0.40
Consensus pattern (23 bp):
TATGTATATGAATATAACTATAT
Found at i:1172407 original size:13 final size:13
Alignment explanation
Indices: 1172389--1172450 Score: 51
Period size: 13 Copynumber: 4.9 Consensus size: 13
1172379 AGATACTATT
1172389 TCCATCACCATAA
1 TCCATCACCATAA
* *
1172402 TCCATCTTCCATTA
1 TCCATC-ACCATAA
1172416 T-CA-CACC-TATA
1 TCCATCACCATA-A
*
1172427 T-CATCACCATAG
1 TCCATCACCATAA
1172439 TCCATCACCATA
1 TCCATCACCATA
1172451 TCACACCTAT
Statistics
Matches: 39, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
10 1 0.03
11 6 0.15
12 6 0.15
13 20 0.51
14 6 0.15
ACGTcount: A:0.32, C:0.37, G:0.02, T:0.29
Consensus pattern (13 bp):
TCCATCACCATAA
Found at i:1172460 original size:35 final size:37
Alignment explanation
Indices: 1172391--1172470 Score: 128
Period size: 35 Copynumber: 2.2 Consensus size: 37
1172381 ATACTATTTC
*
1172391 CATCACCATAATCCATCTTCCATTATCACACCTATAT
1 CATCACCATAATCCATCTACCATTATCACACCTATAT
*
1172428 CATCACCATAGTCCATC-ACCA-TATCACACCTATAT
1 CATCACCATAATCCATCTACCATTATCACACCTATAT
1172463 CATCACCA
1 CATCACCA
1172471 AATTCTCAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
35 22 0.54
36 3 0.07
37 16 0.39
ACGTcount: A:0.34, C:0.38, G:0.01, T:0.28
Consensus pattern (37 bp):
CATCACCATAATCCATCTACCATTATCACACCTATAT
Found at i:1172464 original size:11 final size:11
Alignment explanation
Indices: 1172391--1172470 Score: 65
Period size: 11 Copynumber: 6.7 Consensus size: 11
1172381 ATACTATTTC
1172391 CATCACCATAAT
1 CATCACCAT-AT
*
1172403 CCATCTTCCATTAT
1 -CATC-ACCA-TAT
1172417 CA-CACCTATAT
1 CATCACC-ATAT
1172428 CATCACCATAGT
1 CATCACCATA-T
1172440 CCATCACCATAT
1 -CATCACCATAT
1172452 CA-CACCTATAT
1 CATCACC-ATAT
1172463 CATCACCA
1 CATCACCA
1172471 AATTCTCAAA
Statistics
Matches: 57, Mismatches: 2, Indels: 18
0.74 0.03 0.23
Matches are distributed among these distances:
10 4 0.07
11 19 0.33
12 12 0.21
13 16 0.28
14 5 0.09
15 1 0.02
ACGTcount: A:0.34, C:0.38, G:0.01, T:0.28
Consensus pattern (11 bp):
CATCACCATAT
Found at i:1172468 original size:22 final size:22
Alignment explanation
Indices: 1172391--1172470 Score: 65
Period size: 24 Copynumber: 3.4 Consensus size: 22
1172381 ATACTATTTC
*
1172391 CATCACCATAATCCATCTTCCATTAT
1 CATCACCAT-AT-CATC-ACCA-TAT
1172417 CA-CACCTATATCATCACCATAGT
1 CATCACC-ATATCATCACCATA-T
1172440 CCATCACCATATCA-CACCTATAT
1 -CATCACCATATCATCACC-ATAT
1172463 CATCACCA
1 CATCACCA
1172471 AATTCTCAAA
Statistics
Matches: 48, Mismatches: 1, Indels: 14
0.76 0.02 0.22
Matches are distributed among these distances:
22 10 0.21
23 9 0.19
24 15 0.31
25 10 0.21
26 4 0.08
ACGTcount: A:0.34, C:0.38, G:0.01, T:0.28
Consensus pattern (22 bp):
CATCACCATATCATCACCATAT
Found at i:1175505 original size:13 final size:13
Alignment explanation
Indices: 1175487--1175548 Score: 51
Period size: 13 Copynumber: 4.9 Consensus size: 13
1175477 AGATACTATT
1175487 TCCATCACCATAA
1 TCCATCACCATAA
* *
1175500 TCCATCTTCCATTA
1 TCCATC-ACCATAA
1175514 T-CA-CACC-TATA
1 TCCATCACCATA-A
*
1175525 T-CATCACCATAG
1 TCCATCACCATAA
1175537 TCCATCACCATA
1 TCCATCACCATA
1175549 TCACACCTAT
Statistics
Matches: 39, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
10 1 0.03
11 6 0.15
12 6 0.15
13 20 0.51
14 6 0.15
ACGTcount: A:0.32, C:0.37, G:0.02, T:0.29
Consensus pattern (13 bp):
TCCATCACCATAA
Found at i:1175558 original size:35 final size:37
Alignment explanation
Indices: 1175489--1175568 Score: 128
Period size: 35 Copynumber: 2.2 Consensus size: 37
1175479 ATACTATTTC
*
1175489 CATCACCATAATCCATCTTCCATTATCACACCTATAT
1 CATCACCATAATCCATCTACCATTATCACACCTATAT
*
1175526 CATCACCATAGTCCATC-ACCA-TATCACACCTATAT
1 CATCACCATAATCCATCTACCATTATCACACCTATAT
1175561 CATCACCA
1 CATCACCA
1175569 AATTCTCAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
35 22 0.54
36 3 0.07
37 16 0.39
ACGTcount: A:0.34, C:0.38, G:0.01, T:0.28
Consensus pattern (37 bp):
CATCACCATAATCCATCTACCATTATCACACCTATAT
Found at i:1175562 original size:11 final size:11
Alignment explanation
Indices: 1175489--1175568 Score: 65
Period size: 11 Copynumber: 6.7 Consensus size: 11
1175479 ATACTATTTC
1175489 CATCACCATAAT
1 CATCACCAT-AT
*
1175501 CCATCTTCCATTAT
1 -CATC-ACCA-TAT
1175515 CA-CACCTATAT
1 CATCACC-ATAT
1175526 CATCACCATAGT
1 CATCACCATA-T
1175538 CCATCACCATAT
1 -CATCACCATAT
1175550 CA-CACCTATAT
1 CATCACC-ATAT
1175561 CATCACCA
1 CATCACCA
1175569 AATTCTCAAA
Statistics
Matches: 57, Mismatches: 2, Indels: 18
0.74 0.03 0.23
Matches are distributed among these distances:
10 4 0.07
11 19 0.33
12 12 0.21
13 16 0.28
14 5 0.09
15 1 0.02
ACGTcount: A:0.34, C:0.38, G:0.01, T:0.28
Consensus pattern (11 bp):
CATCACCATAT
Found at i:1175566 original size:22 final size:22
Alignment explanation
Indices: 1175489--1175568 Score: 65
Period size: 24 Copynumber: 3.4 Consensus size: 22
1175479 ATACTATTTC
*
1175489 CATCACCATAATCCATCTTCCATTAT
1 CATCACCAT-AT-CATC-ACCA-TAT
1175515 CA-CACCTATATCATCACCATAGT
1 CATCACC-ATATCATCACCATA-T
1175538 CCATCACCATATCA-CACCTATAT
1 -CATCACCATATCATCACC-ATAT
1175561 CATCACCA
1 CATCACCA
1175569 AATTCTCAAA
Statistics
Matches: 48, Mismatches: 1, Indels: 14
0.76 0.02 0.22
Matches are distributed among these distances:
22 10 0.21
23 9 0.19
24 15 0.31
25 10 0.21
26 4 0.08
ACGTcount: A:0.34, C:0.38, G:0.01, T:0.28
Consensus pattern (22 bp):
CATCACCATATCATCACCATAT
Done.