Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003924.1 Hibiscus syriacus cultivar Beakdansim tig00008483_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: 1466330
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
File 5 of 5
Found at i:1402055 original size:24 final size:24
Alignment explanation
Indices: 1402025--1402097 Score: 83
Period size: 24 Copynumber: 3.0 Consensus size: 24
1402015 ATACATGACC
* *
1402025 TGAATTCTATTCTGATTTCTGATA
1 TGAATTCTGTTTTGATTTCTGATA
* * * * *
1402049 TGGATTCTGTTTTAATATCTGTTC
1 TGAATTCTGTTTTGATTTCTGATA
1402073 TGAATTCTGTTTTGATTTCTGATA
1 TGAATTCTGTTTTGATTTCTGATA
1402097 T
1 T
1402098 CTCCGTTTAA
Statistics
Matches: 37, Mismatches: 12, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.21, C:0.11, G:0.15, T:0.53
Consensus pattern (24 bp):
TGAATTCTGTTTTGATTTCTGATA
Found at i:1402056 original size:48 final size:48
Alignment explanation
Indices: 1402004--1402097 Score: 118
Period size: 48 Copynumber: 2.0 Consensus size: 48
1401994 TTCGACTTGA
*
1402004 ATTCTGTTCTGATA-CATGACCTGAATTCTATTCTGATTTCTGATATGG
1 ATTCTGTTCTAATATC-TGACCTGAATTCTATTCTGATTTCTGATATGG
* ** * *
1402052 ATTCTGTTTTAATATCTGTTCTGAATTCTGTTTTGATTTCTGATAT
1 ATTCTGTTCTAATATCTGACCTGAATTCTATTCTGATTTCTGATAT
1402098 CTCCGTTTAA
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
48 38 0.97
49 1 0.03
ACGTcount: A:0.21, C:0.14, G:0.15, T:0.50
Consensus pattern (48 bp):
ATTCTGTTCTAATATCTGACCTGAATTCTATTCTGATTTCTGATATGG
Found at i:1404173 original size:13 final size:13
Alignment explanation
Indices: 1404155--1404201 Score: 58
Period size: 13 Copynumber: 3.6 Consensus size: 13
1404145 CACAACCCGA
*
1404155 CCGACCCGTTGAC
1 CCGACCCGTTAAC
*
1404168 CCGACCCGTTTAC
1 CCGACCCGTTAAC
**
1404181 CCGACTTGTTAAC
1 CCGACCCGTTAAC
1404194 CCGACCCG
1 CCGACCCG
1404202 ACCCGTTGAC
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
13 28 1.00
ACGTcount: A:0.17, C:0.45, G:0.19, T:0.19
Consensus pattern (13 bp):
CCGACCCGTTAAC
Found at i:1404217 original size:13 final size:14
Alignment explanation
Indices: 1404201--1404246 Score: 58
Period size: 15 Copynumber: 3.2 Consensus size: 14
1404191 AACCCGACCC
1404201 GACCCGTTGAC-TT
1 GACCCGTTGACGTT
1404214 GACCCGTTGACCGTT
1 GACCCGTTGA-CGTT
*
1404229 GACTCGTTGACCGTT
1 GACCCGTTGA-CGTT
1404244 GAC
1 GAC
1404247 TGGCGTTGAC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
13 10 0.33
14 1 0.03
15 19 0.63
ACGTcount: A:0.15, C:0.30, G:0.26, T:0.28
Consensus pattern (14 bp):
GACCCGTTGACGTT
Found at i:1404229 original size:7 final size:7
Alignment explanation
Indices: 1404204--1404246 Score: 54
Period size: 7 Copynumber: 6.1 Consensus size: 7
1404194 CCGACCCGAC
1404204 CCGTTGA
1 CCGTTGA
1404211 -C-TTGA
1 CCGTTGA
1404216 CCCGTTGA
1 -CCGTTGA
1404224 CCGTTGA
1 CCGTTGA
1404231 CTCGTTGA
1 C-CGTTGA
1404239 CCGTTGA
1 CCGTTGA
1404246 C
1 C
1404247 TGGCGTTGAC
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
5 4 0.12
6 1 0.03
7 16 0.50
8 11 0.34
ACGTcount: A:0.14, C:0.30, G:0.26, T:0.30
Consensus pattern (7 bp):
CCGTTGA
Found at i:1404236 original size:15 final size:15
Alignment explanation
Indices: 1404212--1404257 Score: 65
Period size: 15 Copynumber: 2.9 Consensus size: 15
1404202 ACCCGTTGAC
*
1404212 TTGACCCGTTGACCG
1 TTGACTCGTTGACCG
1404227 TTGACTCGTTGACCG
1 TTGACTCGTTGACCG
1404242 TTGACTGGCGTTGACC
1 TTGACT--CGTTGACC
1404258 ACTGTTGACC
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
15 20 0.71
17 8 0.29
ACGTcount: A:0.13, C:0.28, G:0.28, T:0.30
Consensus pattern (15 bp):
TTGACTCGTTGACCG
Found at i:1405582 original size:18 final size:18
Alignment explanation
Indices: 1405556--1405591 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1405546 TCGAAAGGAC
*
1405556 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
1405574 TGAATTAAATAATAAGAT
1 TGAAGTAAATAATAAGAT
1405592 CGGATGGAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.17, T:0.31
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:1406771 original size:48 final size:48
Alignment explanation
Indices: 1406733--1406829 Score: 133
Period size: 48 Copynumber: 2.0 Consensus size: 48
1406723 ATTTTTGACT
1406733 TGAATTCTGTTCTAATA-CATGACCTGAATTCTGTTCTGATTTCTTATA
1 TGAATTCTGTTCTAATATC-TGACCTGAATTCTGTTCTGATTTCTTATA
* ** * *
1406781 TGGATTCTGTTCTAATATCTGTTCTGAATTCTGTTTTGATTTCTGATA
1 TGAATTCTGTTCTAATATCTGACCTGAATTCTGTTCTGATTTCTTATA
1406829 T
1 T
1406830 CTTCGTTTAA
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
48 42 0.98
49 1 0.02
ACGTcount: A:0.22, C:0.14, G:0.14, T:0.49
Consensus pattern (48 bp):
TGAATTCTGTTCTAATATCTGACCTGAATTCTGTTCTGATTTCTTATA
Found at i:1406776 original size:12 final size:12
Alignment explanation
Indices: 1406756--1406825 Score: 54
Period size: 12 Copynumber: 5.8 Consensus size: 12
1406746 AATACATGAC
*
1406756 CTGAATTCTGTT
1 CTGATTTCTGTT
1406768 CTGATTTCT-TAT
1 CTGATTTCTGT-T
*
1406780 ATGGA-TTCTGTT
1 CT-GATTTCTGTT
* *
1406792 CTAATATCTGTT
1 CTGATTTCTGTT
*
1406804 CTGAATTCTGTT
1 CTGATTTCTGTT
*
1406816 TTGATTTCTG
1 CTGATTTCTG
1406826 ATATCTTCGT
Statistics
Matches: 44, Mismatches: 10, Indels: 8
0.71 0.16 0.13
Matches are distributed among these distances:
11 2 0.05
12 39 0.89
13 3 0.07
ACGTcount: A:0.17, C:0.14, G:0.16, T:0.53
Consensus pattern (12 bp):
CTGATTTCTGTT
Found at i:1406787 original size:24 final size:24
Alignment explanation
Indices: 1406757--1406829 Score: 76
Period size: 24 Copynumber: 3.0 Consensus size: 24
1406747 ATACATGACC
1406757 TGAATTCTGTTCTGATTTCTTATA
1 TGAATTCTGTTCTGATTTCTTATA
* * * *
1406781 TGGATTCTGTTCTAATATCTGT-TC
1 TGAATTCTGTTCTGATTTCT-TATA
* *
1406805 TGAATTCTGTTTTGATTTCTGATA
1 TGAATTCTGTTCTGATTTCTTATA
1406829 T
1 T
1406830 CTTCGTTTAA
Statistics
Matches: 37, Mismatches: 10, Indels: 4
0.73 0.20 0.08
Matches are distributed among these distances:
24 36 0.97
25 1 0.03
ACGTcount: A:0.19, C:0.12, G:0.15, T:0.53
Consensus pattern (24 bp):
TGAATTCTGTTCTGATTTCTTATA
Found at i:1406995 original size:2 final size:2
Alignment explanation
Indices: 1406988--1407012 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1406978 GGGATGGGGG
1406988 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 T
1407013 GTTTTAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1422715 original size:13 final size:13
Alignment explanation
Indices: 1422696--1422732 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
1422686 GTCACAATCC
1422696 GACCCGACCCGTT
1 GACCCGACCCGTT
*
1422709 TACCCGACCCGTT
1 GACCCGACCCGTT
1422722 GACCCGACCCG
1 GACCCGACCCG
1422733 ACCCGTTGAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.16, C:0.49, G:0.22, T:0.14
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:1422732 original size:31 final size:31
Alignment explanation
Indices: 1422694--1422758 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 31
1422684 CGGTCACAAT
* *
1422694 CCGACCCGACCCGTTTACCCGACCCGTTGAC
1 CCGACCCGACCCGTTGACCCGACCCGTTCAC
**
1422725 CCGACCCGACCCGTTGACTTGACCCGTTCAC
1 CCGACCCGACCCGTTGACCCGACCCGTTCAC
1422756 CCG
1 CCG
1422759 TTGACCGTTG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.15, C:0.48, G:0.20, T:0.17
Consensus pattern (31 bp):
CCGACCCGACCCGTTGACCCGACCCGTTCAC
Found at i:1422776 original size:15 final size:15
Alignment explanation
Indices: 1422758--1422786 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1422748 CCGTTCACCC
1422758 GTTGACCGTTGACTT
1 GTTGACCGTTGACTT
1422773 GTTGACCGTTGACT
1 GTTGACCGTTGACT
1422787 GGCGTTGACC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.14, C:0.21, G:0.28, T:0.38
Consensus pattern (15 bp):
GTTGACCGTTGACTT
Found at i:1425308 original size:24 final size:24
Alignment explanation
Indices: 1425278--1425350 Score: 83
Period size: 24 Copynumber: 3.0 Consensus size: 24
1425268 ATACATGACC
*
1425278 TGAATTCTATTCTGATTTCTGATA
1 TGAATTCTGTTCTGATTTCTGATA
* * * * *
1425302 TGGATTCTGTTCTAATATCTGTTC
1 TGAATTCTGTTCTGATTTCTGATA
*
1425326 TGAATTCTGTTTTGATTTCTGATA
1 TGAATTCTGTTCTGATTTCTGATA
1425350 T
1 T
1425351 CTCCGTTTAA
Statistics
Matches: 37, Mismatches: 12, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.21, C:0.12, G:0.15, T:0.52
Consensus pattern (24 bp):
TGAATTCTGTTCTGATTTCTGATA
Found at i:1425334 original size:12 final size:12
Alignment explanation
Indices: 1425277--1425346 Score: 61
Period size: 12 Copynumber: 5.8 Consensus size: 12
1425267 GATACATGAC
*
1425277 CTGAATTCTATT
1 CTGAATTCTGTT
* *
1425289 CTGATTTCTGAT
1 CTGAATTCTGTT
* *
1425301 ATGGATTCTGTT
1 CTGAATTCTGTT
1425313 CT-AATATCTGTT
1 CTGAAT-TCTGTT
1425325 CTGAATTCTGTT
1 CTGAATTCTGTT
* *
1425337 TTGATTTCTG
1 CTGAATTCTG
1425347 ATATCTCCGT
Statistics
Matches: 45, Mismatches: 11, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
11 2 0.04
12 40 0.89
13 3 0.07
ACGTcount: A:0.19, C:0.14, G:0.16, T:0.51
Consensus pattern (12 bp):
CTGAATTCTGTT
Found at i:1427388 original size:17 final size:16
Alignment explanation
Indices: 1427368--1427408 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 16
1427358 CGGTCCACAA
1427368 ACCCGACCGACCCGTTG
1 ACCCGACCGA-CCGTTG
*
1427385 ACCCGACCCGACCGTTT
1 ACCCGA-CCGACCGTTG
1427402 ACCCGAC
1 ACCCGAC
1427409 TTGTTAACCC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 1 0.05
17 17 0.77
18 4 0.18
ACGTcount: A:0.20, C:0.49, G:0.20, T:0.12
Consensus pattern (16 bp):
ACCCGACCGACCGTTG
Found at i:1427449 original size:7 final size:7
Alignment explanation
Indices: 1427434--1427468 Score: 52
Period size: 7 Copynumber: 4.7 Consensus size: 7
1427424 GACCCTTGAC
1427434 TTGACCCG
1 TTGA-CCG
1427442 TTGACCG
1 TTGACCG
1427449 TTGACTCG
1 TTGAC-CG
1427457 TTGACCG
1 TTGACCG
1427464 TTGAC
1 TTGAC
1427469 TGGCGTTGAC
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
7 15 0.58
8 11 0.42
ACGTcount: A:0.14, C:0.29, G:0.26, T:0.31
Consensus pattern (7 bp):
TTGACCG
Found at i:1427458 original size:15 final size:15
Alignment explanation
Indices: 1427434--1427479 Score: 65
Period size: 15 Copynumber: 2.9 Consensus size: 15
1427424 GACCCTTGAC
*
1427434 TTGACCCGTTGACCG
1 TTGACTCGTTGACCG
1427449 TTGACTCGTTGACCG
1 TTGACTCGTTGACCG
1427464 TTGACTGGCGTTGACC
1 TTGACT--CGTTGACC
1427480 ACTGTTGACC
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
15 20 0.71
17 8 0.29
ACGTcount: A:0.13, C:0.28, G:0.28, T:0.30
Consensus pattern (15 bp):
TTGACTCGTTGACCG
Found at i:1430564 original size:163 final size:163
Alignment explanation
Indices: 1430294--1430619 Score: 611
Period size: 163 Copynumber: 2.0 Consensus size: 163
1430284 ATCTATCGAC
1430294 TTCAGTAAGGAAGTTCTTCCGGTGTTGTTGCAGAGTATGGTACATGTGATTAGGGGCATGTAATT
1 TTCAGTAAGGAAGTTCTTCCGGTGTTGTTGCAGAGTATGGTACATGTGATTAGGGGCATGTAATT
1430359 GTATTTGTATTATATACGAGCCGTGAAAATCTGTTTATTTTTAAATAGTGGCAAATGATTTTATA
66 GTATTTGTATTATATACGAGCCGTGAAAATCTGTTTATTTTTAAATAGTGGCAAATGATTTTATA
1430424 AGTTACACGTTTCAATAAAAGTTTTAAAATTTT
131 AGTTACACGTTTCAATAAAAGTTTTAAAATTTT
1430457 TTCAGTAAGGAAGTTCTTCCGGTGTTG-TGCAGAGTATGGTACATGTGATTAGGGGGCATGTAAT
1 TTCAGTAAGGAAGTTCTTCCGGTGTTGTTGCAGAGTATGGTACATGTGATTA-GGGGCATGTAAT
*
1430521 TGTATTTGT-TTTTATACGAGCCGTGAAAATCTGTTTTATTTTTAAATAGTGGCAAATGATTTTA
65 TGTATTTGTATTATATACGAGCCGTGAAAATCTG-TTTATTTTTAAATAGTGGCAAATGATTTTA
1430585 TAAGTTACACGTTTCAATAAAAGTTTTAAAATTTT
129 TAAGTTACACGTTTCAATAAAAGTTTTAAAATTTT
1430620 CGTTATTTTT
Statistics
Matches: 160, Mismatches: 1, Indels: 4
0.97 0.01 0.02
Matches are distributed among these distances:
162 47 0.29
163 113 0.71
ACGTcount: A:0.29, C:0.09, G:0.21, T:0.40
Consensus pattern (163 bp):
TTCAGTAAGGAAGTTCTTCCGGTGTTGTTGCAGAGTATGGTACATGTGATTAGGGGCATGTAATT
GTATTTGTATTATATACGAGCCGTGAAAATCTGTTTATTTTTAAATAGTGGCAAATGATTTTATA
AGTTACACGTTTCAATAAAAGTTTTAAAATTTT
Found at i:1437488 original size:7 final size:7
Alignment explanation
Indices: 1437468--1437511 Score: 54
Period size: 7 Copynumber: 6.4 Consensus size: 7
1437458 GTCAAAGGAA
*
1437468 GTCAACA
1 GTCAACG
1437475 GTC-ACG
1 GTCAACG
1437481 GTCAACG
1 GTCAACG
*
1437488 GTCAACA
1 GTCAACG
*
1437495 GTCAATG
1 GTCAACG
1437502 GTCAACG
1 GTCAACG
1437509 GTC
1 GTC
1437512 GGGTCGGGTC
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
6 5 0.16
7 26 0.84
ACGTcount: A:0.30, C:0.27, G:0.25, T:0.18
Consensus pattern (7 bp):
GTCAACG
Found at i:1437506 original size:21 final size:20
Alignment explanation
Indices: 1437468--1437511 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 20
1437458 GTCAAAGGAA
1437468 GTCAACAGTCACGGTCAACG
1 GTCAACAGTCACGGTCAACG
*
1437488 GTCAACAGTCAATGGTCAACG
1 GTCAACAGTC-ACGGTCAACG
1437509 GTC
1 GTC
1437512 GGGTCGGGTC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 10 0.45
21 12 0.55
ACGTcount: A:0.30, C:0.27, G:0.25, T:0.18
Consensus pattern (20 bp):
GTCAACAGTCACGGTCAACG
Found at i:1437518 original size:5 final size:5
Alignment explanation
Indices: 1437508--1437554 Score: 53
Period size: 5 Copynumber: 9.8 Consensus size: 5
1437498 AATGGTCAAC
* * *
1437508 GGTCG GGTCG GGTC- AGTCG GGTCG GGTCA GGTC- AGTCG GGTCG GGTC
1 GGTCG GGTCG GGTCG GGTCG GGTCG GGTCG GGTCG GGTCG GGTCG GGTC
1437555 AGACCGGTCA
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
4 6 0.17
5 29 0.83
ACGTcount: A:0.06, C:0.21, G:0.51, T:0.21
Consensus pattern (5 bp):
GGTCG
Found at i:1437526 original size:14 final size:14
Alignment explanation
Indices: 1437509--1437537 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1437499 ATGGTCAACG
1437509 GTCGGGTCGGGTCA
1 GTCGGGTCGGGTCA
1437523 GTCGGGTCGGGTCA
1 GTCGGGTCGGGTCA
1437537 G
1 G
1437538 GTCAGTCGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.07, C:0.21, G:0.52, T:0.21
Consensus pattern (14 bp):
GTCGGGTCGGGTCA
Found at i:1437532 original size:19 final size:19
Alignment explanation
Indices: 1437508--1437556 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
1437498 AATGGTCAAC
*
1437508 GGTCGGGTCGGGTCAGTCG
1 GGTCGGGTCAGGTCAGTCG
1437527 GGTCGGGTCAGGTCAGTCG
1 GGTCGGGTCAGGTCAGTCG
1437546 GGTCGGGTCAG
1 GGTCGGGTCAG
1437557 ACCGGTCAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.08, C:0.20, G:0.51, T:0.20
Consensus pattern (19 bp):
GGTCGGGTCAGGTCAGTCG
Found at i:1437545 original size:14 final size:14
Alignment explanation
Indices: 1437514--1437556 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
1437504 CAACGGTCGG
*
1437514 GTCGGGTCA-GTCGG
1 GTCGGGTCAGGTC-A
1437528 GTCGGGTCAGGTCA
1 GTCGGGTCAGGTCA
*
1437542 GTCGGGTCGGGTCA
1 GTCGGGTCAGGTCA
1437556 G
1 G
1437557 ACCGGTCAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
14 23 0.88
15 3 0.12
ACGTcount: A:0.09, C:0.21, G:0.49, T:0.21
Consensus pattern (14 bp):
GTCGGGTCAGGTCA
Found at i:1437578 original size:18 final size:19
Alignment explanation
Indices: 1437551--1437595 Score: 65
Period size: 18 Copynumber: 2.4 Consensus size: 19
1437541 AGTCGGGTCG
*
1437551 GGTCAGACCGGTCAAAAT-
1 GGTCAAACCGGTCAAAATC
*
1437569 GGTCAAACCGGTCGAAATC
1 GGTCAAACCGGTCAAAATC
1437588 GGTCAAAC
1 GGTCAAAC
1437596 TGATTTCCAG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 16 0.67
19 8 0.33
ACGTcount: A:0.33, C:0.24, G:0.27, T:0.16
Consensus pattern (19 bp):
GGTCAAACCGGTCAAAATC
Found at i:1444721 original size:13 final size:13
Alignment explanation
Indices: 1444703--1444727 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1444693 GGTCAAAGGA
1444703 AGTCAACGGTCAC
1 AGTCAACGGTCAC
1444716 AGTCAACGGTCA
1 AGTCAACGGTCA
1444728 ACGGTCGGGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.28, G:0.24, T:0.16
Consensus pattern (13 bp):
AGTCAACGGTCAC
Found at i:1444771 original size:19 final size:19
Alignment explanation
Indices: 1444729--1444771 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
1444719 CAACGGTCAA
**
1444729 CGGTCGGGTCGGGTCAGTT
1 CGGTCGGGTCGGGTCAGAC
*
1444748 GGGTCGGGTCGGGTCAGAC
1 CGGTCGGGTCGGGTCAGAC
1444767 CGGTC
1 CGGTC
1444772 AAACCAGTTC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.07, C:0.23, G:0.49, T:0.21
Consensus pattern (19 bp):
CGGTCGGGTCGGGTCAGAC
Found at i:1444817 original size:29 final size:31
Alignment explanation
Indices: 1444784--1444858 Score: 93
Period size: 29 Copynumber: 2.5 Consensus size: 31
1444774 ACCAGTTCAG
**
1444784 ACCGGTCAAACCGGTTC-GAACCGG-TCGAA
1 ACCGGTCAAACCGGTTCAGAACCGGTTAAAA
*
1444813 ACCGGTCAAACCAG-TCAGAACCGGTTAAAA
1 ACCGGTCAAACCGGTTCAGAACCGGTTAAAA
*
1444843 ACTGGTCAAACCGGTT
1 ACCGGTCAAACCGGTT
1444859 TCCAGCCCTC
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
28 2 0.05
29 20 0.53
30 15 0.39
31 1 0.03
ACGTcount: A:0.32, C:0.28, G:0.24, T:0.16
Consensus pattern (31 bp):
ACCGGTCAAACCGGTTCAGAACCGGTTAAAA
Found at i:1444819 original size:10 final size:9
Alignment explanation
Indices: 1444759--1444857 Score: 81
Period size: 9 Copynumber: 10.3 Consensus size: 9
1444749 GGTCGGGTCG
*
1444759 GGTCAGACC
1 GGTCAAACC
1444768 GGTCAAACC
1 GGTCAAACC
* *
1444777 AGTTCAGACC
1 -GGTCAAACC
1444787 GGTCAAACC
1 GGTCAAACC
*
1444796 GGTTCGAACC
1 GG-TCAAACC
1444806 GGTCGAAACC
1 GGTC-AAACC
1444816 GGTCAAACC
1 GGTCAAACC
*
1444825 AGTCAGAACC
1 GGTCA-AACC
* *
1444835 GGTTAAAAACT
1 GG-T-CAAACC
1444846 GGTCAAACC
1 GGTCAAACC
1444855 GGT
1 GGT
1444858 TTCCAGCCCT
Statistics
Matches: 71, Mismatches: 13, Indels: 12
0.74 0.14 0.12
Matches are distributed among these distances:
9 35 0.49
10 29 0.41
11 6 0.08
12 1 0.01
ACGTcount: A:0.31, C:0.28, G:0.25, T:0.15
Consensus pattern (9 bp):
GGTCAAACC
Found at i:1444824 original size:19 final size:18
Alignment explanation
Indices: 1444759--1444857 Score: 81
Period size: 19 Copynumber: 5.2 Consensus size: 18
1444749 GGTCGGGTCG
*
1444759 GGTCAGACCGGTCAAACC
1 GGTCAAACCGGTCAAACC
* *
1444777 AGTTCAGACCGGTCAAACC
1 -GGTCAAACCGGTCAAACC
*
1444796 GGTTCGAACCGGTCGAAACC
1 GG-TCAAACCGGTC-AAACC
*
1444816 GGTCAAACCAGTCAGAACC
1 GGTCAAACCGGTCA-AACC
* *
1444835 GGTTAAAAACTGGTCAAACC
1 GG-T-CAAACCGGTCAAACC
1444855 GGT
1 GGT
1444858 TTCCAGCCCT
Statistics
Matches: 66, Mismatches: 9, Indels: 10
0.78 0.11 0.12
Matches are distributed among these distances:
18 2 0.03
19 42 0.64
20 14 0.21
21 8 0.12
ACGTcount: A:0.31, C:0.28, G:0.25, T:0.15
Consensus pattern (18 bp):
GGTCAAACCGGTCAAACC
Found at i:1445440 original size:303 final size:303
Alignment explanation
Indices: 1444893--1445499 Score: 1000
Period size: 303 Copynumber: 2.0 Consensus size: 303
1444883 CGGCGCGTGT
* *
1444893 GGCGCGTGAGGCCTCCTACGGGGGTCTAAAAATTTCGGAAAATTTTCTAAAAAAAATTTTAAGCG
1 GGCGCGTGAGGCCTCCTACAGGGGTCTAAAAATTTCGGAAAATTTTCTAAAAAAAATGTTAAGCG
1444958 ATTTCGAGATACTTACAAAGATCGGTTCAAATTTTTGAACGGCGGAGAGCTCGATTTCAACTCAG
66 ATTTCGAGATACTTACAAAGATCGGTTCAAATTTTTGAACGGCGGAGAGCTCGATTTCAACTCAG
* * * * *
1445023 CCGAATCTTTGACTGCTTCACCTCCTCACGCGCCGCTGTCGATGGCGAACAAGGTTGACACCGAC
131 CCGAATCTTTGACTGCTCCACCTCCTCACGCACCGCCGTCGACGACGAACAAGGTTGACACCGAC
* * *
1445088 TGACACGAAACGACACAAGGAACACGATGGTGTAGGAGGTGTCGTAAACGGAGCAACGATCGGCA
196 GGACACGAAACGACACAAGGAACACGATGGTGCAGGAGGTGTCGTAAACGGAGCAACGATCGACA
**
1445153 GTGAATTTAAGATTTTCCCGGTGATAGAGCTAACAAAAACGTC
261 GTGAATTTAAGATTTTCCCGACGATAGAGCTAACAAAAACGTC
* * **
1445196 GGCGCGTGAGGCCTCCTCCAGGGGTCTAAAAATTTTGGAGAAA-TTTCTAAAAATTATGTTAAGC
1 GGCGCGTGAGGCCTCCTACAGGGGTCTAAAAATTTCGGA-AAATTTTCTAAAAAAAATGTTAAGC
* *
1445260 GATTTCGAGATACTTACAAAGATCGGTTCAAATTTTTGAACGGTGGAGAGCTCGATTTCAACTCG
65 GATTTCGAGATACTTACAAAGATCGGTTCAAATTTTTGAACGGCGGAGAGCTCGATTTCAACTCA
*
1445325 GCCGAATCTTTGACTGCTCCACCTCCTCACGCACCGCCGTCGACGACGAACAAGGTTGACACCGG
130 GCCGAATCTTTGACTGCTCCACCTCCTCACGCACCGCCGTCGACGACGAACAAGGTTGACACCGA
* *
1445390 CGGACTCGAAACGACACAAGGAACACGATGGTGCAGGAGGTGTCGTAAACGGAGCAACGATCGAT
195 CGGACACGAAACGACACAAGGAACACGATGGTGCAGGAGGTGTCGTAAACGGAGCAACGATCGAC
*
1445455 GGTGAATTTAAGATTTTCCCGACGATAGAGCTAACAAAAACGTC
260 AGTGAATTTAAGATTTTCCCGACGATAGAGCTAACAAAAACGTC
1445499 G
1 G
1445500 AGACTTTGAC
Statistics
Matches: 281, Mismatches: 22, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
303 278 0.99
304 3 0.01
ACGTcount: A:0.30, C:0.22, G:0.25, T:0.23
Consensus pattern (303 bp):
GGCGCGTGAGGCCTCCTACAGGGGTCTAAAAATTTCGGAAAATTTTCTAAAAAAAATGTTAAGCG
ATTTCGAGATACTTACAAAGATCGGTTCAAATTTTTGAACGGCGGAGAGCTCGATTTCAACTCAG
CCGAATCTTTGACTGCTCCACCTCCTCACGCACCGCCGTCGACGACGAACAAGGTTGACACCGAC
GGACACGAAACGACACAAGGAACACGATGGTGCAGGAGGTGTCGTAAACGGAGCAACGATCGACA
GTGAATTTAAGATTTTCCCGACGATAGAGCTAACAAAAACGTC
Found at i:1447861 original size:4 final size:4
Alignment explanation
Indices: 1447841--1447928 Score: 59
Period size: 4 Copynumber: 20.2 Consensus size: 4
1447831 AAGCAGTTGA
* * *
1447841 ACCG ACCG AGCCA ACCG ACCG AGCCG ACCG ACCG ACTG AGCCG ACCG AGTCG
1 ACCG ACCG A-CCG ACCG ACCG A-CCG ACCG ACCG ACCG A-CCG ACCG A-CCG
* * *
1447893 ACCG AGCCG ACCT AGCCG ATCG ATCG AGCCG ACCG A
1 ACCG A-CCG ACCG A-CCG ACCG ACCG A-CCG ACCG A
1447929 GCTGATCGAC
Statistics
Matches: 67, Mismatches: 10, Indels: 14
0.74 0.11 0.15
Matches are distributed among these distances:
4 44 0.66
5 23 0.34
ACGTcount: A:0.25, C:0.41, G:0.28, T:0.06
Consensus pattern (4 bp):
ACCG
Found at i:1447867 original size:9 final size:9
Alignment explanation
Indices: 1447855--1447976 Score: 83
Period size: 9 Copynumber: 13.3 Consensus size: 9
1447845 ACCGAGCCAA
1447855 CCGACCGAG
1 CCGACCGAG
1447864 CCGACCGA-
1 CCGACCGAG
*
1447872 CCGACTGAG
1 CCGACCGAG
1447881 CCGACCGAG
1 CCGACCGAG
*
1447890 TCGACCGAG
1 CCGACCGAG
*
1447899 CCGACCTAG
1 CCGACCGAG
1447908 CCGATCGATCGAG
1 CCGA-C---CGAG
1447921 CCGACCGAG
1 CCGACCGAG
* *
1447930 CTGATCGA-
1 CCGACCGAG
1447938 CCGA--GATGG
1 CCGACCGA--G
*
1447947 CCGAGCTGA-
1 CCGA-CCGAG
1447956 CCGACCGAG
1 CCGACCGAG
*
1447965 CCGATCGAG
1 CCGACCGAG
1447974 CCG
1 CCG
1447977 CATGGACTGG
Statistics
Matches: 90, Mismatches: 11, Indels: 24
0.72 0.09 0.19
Matches are distributed among these distances:
6 2 0.02
8 13 0.14
9 64 0.71
10 1 0.01
12 3 0.03
13 7 0.08
ACGTcount: A:0.22, C:0.38, G:0.32, T:0.08
Consensus pattern (9 bp):
CCGACCGAG
Found at i:1447884 original size:22 final size:22
Alignment explanation
Indices: 1447842--1447976 Score: 105
Period size: 22 Copynumber: 6.1 Consensus size: 22
1447832 AGCAGTTGAA
*
1447842 CCGACCGAGCC-AACCGACCGAG
1 CCGACCGA-CCGAGCCGACCGAG
*
1447864 CCGACCGACCGA-CTGAGCCGA-
1 CCGACCGACCGAGCCGA-CCGAG
* *
1447885 CCGAGTCGACCGAGCCGACCTAG
1 CCGA-CCGACCGAGCCGACCGAG
* *
1447908 CCGATCGATCGAGCCGACCGAG
1 CCGACCGACCGAGCCGACCGAG
* * ** *
1447930 CTGATCGACCGAGATGGCCGAG
1 CCGACCGACCGAGCCGACCGAG
* *
1447952 CTGACCGACCGAGCCGATCGAG
1 CCGACCGACCGAGCCGACCGAG
1447974 CCG
1 CCG
1447977 CATGGACTGG
Statistics
Matches: 91, Mismatches: 17, Indels: 10
0.77 0.14 0.08
Matches are distributed among these distances:
21 9 0.10
22 75 0.82
23 7 0.08
ACGTcount: A:0.23, C:0.39, G:0.31, T:0.07
Consensus pattern (22 bp):
CCGACCGACCGAGCCGACCGAG
Found at i:1447965 original size:13 final size:13
Alignment explanation
Indices: 1447841--1447965 Score: 77
Period size: 13 Copynumber: 9.8 Consensus size: 13
1447831 AAGCAGTTGA
**
1447841 ACCGACCGAGCCA
1 ACCGACCGAGCTG
*
1447854 ACCGACCGAGCCG
1 ACCGACCGAGCTG
1447867 ACCGACCGA-CTG
1 ACCGACCGAGCTG
1447879 AGCCGACCGAG-TCG
1 A-CCGACCGAGCT-G
*
1447893 ACCGAGCCGACCT-
1 ACCGA-CCGAGCTG
* *
1447906 AGCCGATCGATC-G
1 A-CCGACCGAGCTG
1447919 AGCCGACCGAGCTG
1 A-CCGACCGAGCTG
* *
1447933 ATCGACCGAGATG
1 ACCGACCGAGCTG
1447946 ---G-CCGAGCTG
1 ACCGACCGAGCTG
1447955 ACCGACCGAGC
1 ACCGACCGAGC
1447966 CGATCGAGCC
Statistics
Matches: 90, Mismatches: 10, Indels: 24
0.73 0.08 0.19
Matches are distributed among these distances:
9 7 0.08
10 1 0.01
12 4 0.04
13 65 0.72
14 12 0.13
15 1 0.01
ACGTcount: A:0.24, C:0.38, G:0.30, T:0.07
Consensus pattern (13 bp):
ACCGACCGAGCTG
Found at i:1448032 original size:19 final size:19
Alignment explanation
Indices: 1447990--1448036 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 19
1447980 GGACTGGACC
* *
1447990 GCCTGGACCGGACCGATCA
1 GCCTGGACCAGACCGAACA
*
1448009 GCCTGGACCAGACCGAACC
1 GCCTGGACCAGACCGAACA
*
1448028 TCCTGGACC
1 GCCTGGACC
1448037 GAACCGTTGA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.21, C:0.40, G:0.28, T:0.11
Consensus pattern (19 bp):
GCCTGGACCAGACCGAACA
Found at i:1448042 original size:19 final size:19
Alignment explanation
Indices: 1447990--1448042 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 19
1447980 GGACTGGACC
* *
1447990 GCCTGGACCGGACCGATCA
1 GCCTGGACCGAACCGAACA
*
1448009 GCCTGGACC-AGACCGAACC
1 GCCTGGACCGA-ACCGAACA
*
1448028 TCCTGGACCGAACCG
1 GCCTGGACCGAACCG
1448043 TTGACCGTTG
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
19 27 0.96
20 1 0.04
ACGTcount: A:0.23, C:0.40, G:0.28, T:0.09
Consensus pattern (19 bp):
GCCTGGACCGAACCGAACA
Found at i:1456318 original size:21 final size:19
Alignment explanation
Indices: 1456294--1456336 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
1456284 AACCTTACTC
1456294 TTTCTAAAATTTTGTAAAATA
1 TTTCT-AAATTTT-TAAAATA
* *
1456315 TTTCTTAATTTTTAAACTA
1 TTTCTAAATTTTTAAAATA
1456334 TTT
1 TTT
1456337 TCCAAAATGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 9 0.45
20 6 0.30
21 5 0.25
ACGTcount: A:0.35, C:0.07, G:0.02, T:0.56
Consensus pattern (19 bp):
TTTCTAAATTTTTAAAATA
Done.