Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008199.1 Hibiscus syriacus cultivar Beakdansim tig00110819_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: 2638622
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 11 of 11
Found at i:2494295 original size:116 final size:116
Alignment explanation
Indices: 2494153--2494386 Score: 468
Period size: 116 Copynumber: 2.0 Consensus size: 116
2494143 CTTGAGGGTG
2494153 TATATGTAGTGATATGTACATACATGTTCCTGTACTTCGATGAAGCACTTCCTATTTATATTTAA
1 TATATGTAGTGATATGTACATACATGTTCCTGTACTTCGATGAAGCACTTCCTATTTATATTTAA
2494218 ATGTCGCAAAATCAATCTTATGACATCTAGAAGTGTTGTAGTTTCCTGAAT
66 ATGTCGCAAAATCAATCTTATGACATCTAGAAGTGTTGTAGTTTCCTGAAT
2494269 TATATGTAGTGATATGTACATACATGTTCCTGTACTTCGATGAAGCACTTCCTATTTATATTTAA
1 TATATGTAGTGATATGTACATACATGTTCCTGTACTTCGATGAAGCACTTCCTATTTATATTTAA
2494334 ATGTCGCAAAATCAATCTTATGACATCTAGAAGTGTTGTAGTTTCCTGAAT
66 ATGTCGCAAAATCAATCTTATGACATCTAGAAGTGTTGTAGTTTCCTGAAT
2494385 TA
1 TA
2494387 CCCTTCATTT
Statistics
Matches: 118, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
116 118 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.39
Consensus pattern (116 bp):
TATATGTAGTGATATGTACATACATGTTCCTGTACTTCGATGAAGCACTTCCTATTTATATTTAA
ATGTCGCAAAATCAATCTTATGACATCTAGAAGTGTTGTAGTTTCCTGAAT
Found at i:2496421 original size:20 final size:20
Alignment explanation
Indices: 2496396--2496435 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
2496386 AGCAACAGAA
*
2496396 TAAAAATGATTCTATCTAAT
1 TAAAAATGATCCTATCTAAT
2496416 TAAAAATGATCCTATCTAAT
1 TAAAAATGATCCTATCTAAT
2496436 AACTAATAGA
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:0.45, C:0.12, G:0.05, T:0.38
Consensus pattern (20 bp):
TAAAAATGATCCTATCTAAT
Found at i:2496464 original size:53 final size:52
Alignment explanation
Indices: 2496392--2496541 Score: 266
Period size: 53 Copynumber: 2.9 Consensus size: 52
2496382 AATTAGCAAC
2496392 AGAATAAAAA-TGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAAT
1 AGAATAAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAAT
2496443 AGAATAAAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAAT
1 AGAAT-AAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAAT
* *
2496496 AGAATAAGAACTGATTCTATCTAATTAAAACTGATCCTATCTAATA
1 AGAATAAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATA
2496542 TTTAATTTAG
Statistics
Matches: 95, Mismatches: 2, Indels: 3
0.95 0.02 0.03
Matches are distributed among these distances:
51 5 0.05
52 44 0.46
53 46 0.48
ACGTcount: A:0.47, C:0.13, G:0.07, T:0.33
Consensus pattern (52 bp):
AGAATAAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAAT
Found at i:2496478 original size:20 final size:21
Alignment explanation
Indices: 2496449--2496488 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
2496439 TAATAGAATA
*
2496449 AAAAACTGATTCTATCTAATT
1 AAAAACTGATCCTATCTAATT
2496470 AAAAA-TGATCCTATCTAAT
1 AAAAACTGATCCTATCTAAT
2496489 AACTAATAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.45, C:0.15, G:0.05, T:0.35
Consensus pattern (21 bp):
AAAAACTGATCCTATCTAATT
Found at i:2501602 original size:19 final size:20
Alignment explanation
Indices: 2501575--2501619 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
2501565 ATTAGCAACA
**
2501575 TAAT-AAAAATGATTCTATC
1 TAATAAAAAATGACCCTATC
*
2501594 TAATTAAAAATGACCCTATC
1 TAATAAAAAATGACCCTATC
2501614 TAATAA
1 TAATAA
2501620 CTAATAAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 4 0.18
20 18 0.82
ACGTcount: A:0.49, C:0.13, G:0.04, T:0.33
Consensus pattern (20 bp):
TAATAAAAAATGACCCTATC
Found at i:2501603 original size:20 final size:20
Alignment explanation
Indices: 2501578--2501617 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
2501568 AGCAACATAA
**
2501578 TAAAAATGATTCTATCTAAT
1 TAAAAATGACCCTATCTAAT
2501598 TAAAAATGACCCTATCTAAT
1 TAAAAATGACCCTATCTAAT
2501618 AACTAATAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.45, C:0.15, G:0.05, T:0.35
Consensus pattern (20 bp):
TAAAAATGACCCTATCTAAT
Found at i:2501660 original size:20 final size:21
Alignment explanation
Indices: 2501631--2501670 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
2501621 TAATAAAATA
*
2501631 AAAAACTGATTCTATCTAATT
1 AAAAACTGATCCTATCTAATT
2501652 AAAAA-TGATCCTATCTAAT
1 AAAAACTGATCCTATCTAAT
2501671 AACTAATAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.45, C:0.15, G:0.05, T:0.35
Consensus pattern (21 bp):
AAAAACTGATCCTATCTAATT
Found at i:2501709 original size:20 final size:20
Alignment explanation
Indices: 2501684--2501722 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
2501674 TAATAGAATA
*
2501684 AAAACTGATTCTATCTAATT
1 AAAACTGATCCTATCTAATT
2501704 AAAACTGATCCTATCTAAT
1 AAAACTGATCCTATCTAAT
2501723 ATTTAATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.41, C:0.18, G:0.05, T:0.36
Consensus pattern (20 bp):
AAAACTGATCCTATCTAATT
Found at i:2501713 original size:52 final size:52
Alignment explanation
Indices: 2501576--2501723 Score: 253
Period size: 52 Copynumber: 2.8 Consensus size: 52
2501566 TTAGCAACAT
*
2501576 AATAAAAA-TGATTCTATCTAATTAAAAATGACCCTATCTAATAACTAATAA
1 AATAAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAATAA
*
2501627 AATAAAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAATAG
1 AAT-AAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAATAA
*
2501680 AATAAAAACTGATTCTATCTAATTAAAACTGATCCTATCTAATA
1 AATAAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATA
2501724 TTTAATTTAG
Statistics
Matches: 92, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
51 3 0.03
52 45 0.49
53 44 0.48
ACGTcount: A:0.49, C:0.14, G:0.05, T:0.32
Consensus pattern (52 bp):
AATAAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAATAA
Found at i:2505752 original size:31 final size:32
Alignment explanation
Indices: 2505717--2505780 Score: 121
Period size: 31 Copynumber: 2.0 Consensus size: 32
2505707 AATTCGGTGA
2505717 ATTCAATATGTCCTTCTCAC-TAGGAACTCCC
1 ATTCAATATGTCCTTCTCACTTAGGAACTCCC
2505748 ATTCAATATGTCCTTCTCACTTAGGAACTCCC
1 ATTCAATATGTCCTTCTCACTTAGGAACTCCC
2505780 A
1 A
2505781 AACTCTTGGG
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 20 0.62
32 12 0.38
ACGTcount: A:0.27, C:0.31, G:0.09, T:0.33
Consensus pattern (32 bp):
ATTCAATATGTCCTTCTCACTTAGGAACTCCC
Found at i:2534722 original size:47 final size:45
Alignment explanation
Indices: 2534668--2534759 Score: 139
Period size: 47 Copynumber: 2.0 Consensus size: 45
2534658 GTATCAGCTA
2534668 CCTCGTTCATTTTCAAGGTAATGAAGAAGTAGCCTCTTTCTTCATAT
1 CCTCGTTCATTTTCAAGGT-ATGAAGAAGTAGCC-CTTTCTTCATAT
* * *
2534715 CCTCGTTCATTTTGAAGGTATGAAGAATTAGCCCTTTCTTTATAT
1 CCTCGTTCATTTTCAAGGTATGAAGAAGTAGCCCTTTCTTCATAT
2534760 TGTGCTCAGC
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
45 11 0.26
46 13 0.31
47 18 0.43
ACGTcount: A:0.25, C:0.20, G:0.15, T:0.40
Consensus pattern (45 bp):
CCTCGTTCATTTTCAAGGTATGAAGAAGTAGCCCTTTCTTCATAT
Found at i:2535587 original size:3 final size:3
Alignment explanation
Indices: 2535581--2535610 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
2535571 GATTTTTTTT
2535581 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
2535611 CTAATTACAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:2538465 original size:9 final size:9
Alignment explanation
Indices: 2538451--2538480 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
2538441 TTTCAAAACT
2538451 CAAATATTC
1 CAAATATTC
2538460 CAAATATTC
1 CAAATATTC
2538469 CAAAATATTC
1 C-AAATATTC
2538479 CA
1 CA
2538481 TTCTACCTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 11 0.55
10 9 0.45
ACGTcount: A:0.47, C:0.23, G:0.00, T:0.30
Consensus pattern (9 bp):
CAAATATTC
Found at i:2538476 original size:10 final size:10
Alignment explanation
Indices: 2538452--2538480 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
2538442 TTCAAAACTC
2538452 AAATATTCC-
1 AAATATTCCA
2538461 AAATATTCCA
1 AAATATTCCA
2538471 AAATATTCCA
1 AAATATTCCA
2538481 TTCTACCTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 9 0.47
10 10 0.53
ACGTcount: A:0.48, C:0.21, G:0.00, T:0.31
Consensus pattern (10 bp):
AAATATTCCA
Found at i:2540763 original size:42 final size:42
Alignment explanation
Indices: 2540704--2540811 Score: 180
Period size: 42 Copynumber: 2.6 Consensus size: 42
2540694 TTTTTCCGTT
* *
2540704 TTTCACGAAATTCGTTTTTCGGAAAATGTTTTCCCGTGTTTG
1 TTTCACGTAATTCGTTTTTCGGAAAACGTTTTCCCGTGTTTG
2540746 TTTCACGTAATTCGTTTTTCGGAAAACGTTTTCCCGTGTTTG
1 TTTCACGTAATTCGTTTTTCGGAAAACGTTTTCCCGTGTTTG
* *
2540788 TTTCACGTAATTCATTTTCCGGAA
1 TTTCACGTAATTCGTTTTTCGGAA
2540812 TGTAATTCAT
Statistics
Matches: 62, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 62 1.00
ACGTcount: A:0.19, C:0.19, G:0.18, T:0.44
Consensus pattern (42 bp):
TTTCACGTAATTCGTTTTTCGGAAAACGTTTTCCCGTGTTTG
Found at i:2540883 original size:14 final size:14
Alignment explanation
Indices: 2540864--2540891 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2540854 ACTTACGAAT
2540864 TCATTTTCCGTAAG
1 TCATTTTCCGTAAG
2540878 TCATTTTCCGTAAG
1 TCATTTTCCGTAAG
2540892 CAAAAATACT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.21, G:0.14, T:0.43
Consensus pattern (14 bp):
TCATTTTCCGTAAG
Found at i:2541053 original size:31 final size:31
Alignment explanation
Indices: 2540989--2541060 Score: 87
Period size: 31 Copynumber: 2.4 Consensus size: 31
2540979 ATATTTAAAA
2540989 TATATTTATAATATTTATAATAATATAATAT
1 TATATTTATAATATTTATAATAATATAATAT
* *
2541020 TATATTTTTAATA-TTAT-ATAAAATAATCAAT
1 TATATTTATAATATTTATAATAATATAAT--AT
2541051 TATA-TTATAA
1 TATATTTATAA
2541061 ATAAAGATTA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
29 9 0.25
30 9 0.25
31 18 0.50
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (31 bp):
TATATTTATAATATTTATAATAATATAATAT
Found at i:2541133 original size:53 final size:55
Alignment explanation
Indices: 2540978--2541142 Score: 130
Period size: 53 Copynumber: 3.1 Consensus size: 55
2540968 TTAATTATTA
* * * *
2540978 AATATTTAAAAT-AT-ATTTATAATATTTATAATAATATAATATTATAT-TTTTAAT
1 AATATATAAAATAATCAATTAT-ATATATATAATGA-ATAATATTATATATTTTAAT
* * * *
2541032 ATTATATAAAATAATCAATTATATTATAAATAAAGATTAAT-TT-T-TATTTTAAT
1 AATATATAAAATAATCAATTATA-TATATATAATGAATAATATTATATATTTTAAT
* ** * *
2541085 AATATATAATA-AAT-TTTTTTATATATATAATGAATAATATTATATATTTCAAT
1 AATATATAAAATAATCAATTATATATATATAATGAATAATATTATATATTTTAAT
2541138 AATAT
1 AATAT
2541143 TTTAGTAAAG
Statistics
Matches: 87, Mismatches: 17, Indels: 15
0.73 0.14 0.13
Matches are distributed among these distances:
50 14 0.16
51 6 0.07
52 5 0.06
53 30 0.34
54 12 0.14
55 7 0.08
56 13 0.15
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (55 bp):
AATATATAAAATAATCAATTATATATATATAATGAATAATATTATATATTTTAAT
Found at i:2541380 original size:20 final size:20
Alignment explanation
Indices: 2541303--2541371 Score: 113
Period size: 20 Copynumber: 3.5 Consensus size: 20
2541293 TTTTCAGATG
2541303 TTTTCCAGAAATG-AATTCA
1 TTTTCCAGAAATGTAATTCA
*
2541322 TTTTCCATAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
*
2541342 TTTTACAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
2541362 TTTTCCAGAA
1 TTTTCCAGAA
2541372 TTCAAATTCC
Statistics
Matches: 45, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
19 12 0.27
20 33 0.73
ACGTcount: A:0.36, C:0.14, G:0.09, T:0.41
Consensus pattern (20 bp):
TTTTCCAGAAATGTAATTCA
Found at i:2541380 original size:40 final size:39
Alignment explanation
Indices: 2541303--2541380 Score: 102
Period size: 40 Copynumber: 2.0 Consensus size: 39
2541293 TTTTCAGATG
* * **
2541303 TTTTCCAGAAATGAATTCATTTTCCATAAATGTAATTCA
1 TTTTACAGAAATGAATTCATTTTCCAGAAATCAAATTCA
*
2541342 TTTTACAGAAATGTAATTCATTTTCCAGAATTCAAATTC
1 TTTTACAGAAATG-AATTCATTTTCCAGAAATCAAATTC
2541381 CAGTAATTCA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
39 12 0.36
40 21 0.64
ACGTcount: A:0.36, C:0.15, G:0.08, T:0.41
Consensus pattern (39 bp):
TTTTACAGAAATGAATTCATTTTCCAGAAATCAAATTCA
Found at i:2541390 original size:15 final size:15
Alignment explanation
Indices: 2541354--2541435 Score: 112
Period size: 15 Copynumber: 5.5 Consensus size: 15
2541344 TTACAGAAAT
**
2541354 GTAATTCATTTTCCA
1 GTAATTCAAATTCCA
2541369 G-AATTCAAATTCCA
1 GTAATTCAAATTCCA
**
2541383 GTAATTCATTTTCCA
1 GTAATTCAAATTCCA
2541398 GTAATTCAAATTCCA
1 GTAATTCAAATTCCA
*
2541413 GTAATTCAAATTTCA
1 GTAATTCAAATTCCA
2541428 GTAATTCA
1 GTAATTCA
2541436 TTTTCTGGAA
Statistics
Matches: 59, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
14 12 0.20
15 47 0.80
ACGTcount: A:0.35, C:0.18, G:0.07, T:0.39
Consensus pattern (15 bp):
GTAATTCAAATTCCA
Found at i:2541406 original size:30 final size:30
Alignment explanation
Indices: 2541354--2541435 Score: 132
Period size: 30 Copynumber: 2.8 Consensus size: 30
2541344 TTACAGAAAT
2541354 GTAATTCATTTTCCAG-AATTCAAATTCCA
1 GTAATTCATTTTCCAGTAATTCAAATTCCA
2541383 GTAATTCATTTTCCAGTAATTCAAATTCCA
1 GTAATTCATTTTCCAGTAATTCAAATTCCA
*
2541413 GTAATTCAAATTT-CAGTAATTCA
1 GTAATTC-ATTTTCCAGTAATTCA
2541436 TTTTCTGGAA
Statistics
Matches: 50, Mismatches: 1, Indels: 3
0.93 0.02 0.06
Matches are distributed among these distances:
29 16 0.32
30 30 0.60
31 4 0.08
ACGTcount: A:0.35, C:0.18, G:0.07, T:0.39
Consensus pattern (30 bp):
GTAATTCATTTTCCAGTAATTCAAATTCCA
Found at i:2541430 original size:45 final size:44
Alignment explanation
Indices: 2541354--2541440 Score: 138
Period size: 45 Copynumber: 2.0 Consensus size: 44
2541344 TTACAGAAAT
**
2541354 GTAATTCATTTTCCAGAATTCAAATTCCAGTAATTCATTTTCCA
1 GTAATTCAAATTCCAGAATTCAAATTCCAGTAATTCATTTTCCA
*
2541398 GTAATTCAAATTCCAGTAATTCAAATTTCAGTAATTCATTTTC
1 GTAATTCAAATTCCAG-AATTCAAATTCCAGTAATTCATTTTC
2541441 TGGAAAACCA
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
44 14 0.36
45 25 0.64
ACGTcount: A:0.33, C:0.18, G:0.07, T:0.41
Consensus pattern (44 bp):
GTAATTCAAATTCCAGAATTCAAATTCCAGTAATTCATTTTCCA
Found at i:2541812 original size:7 final size:7
Alignment explanation
Indices: 2541802--2541869 Score: 84
Period size: 7 Copynumber: 9.7 Consensus size: 7
2541792 AACTTAAATT
2541802 CTAAACC
1 CTAAACC
2541809 CTAAACC
1 CTAAACC
2541816 CTAAACC
1 CTAAACC
*
2541823 CTAATCC
1 CTAAACC
*
2541830 CTAATCC
1 CTAAACC
2541837 CTAATA-C
1 CTAA-ACC
*
2541844 ATAAACC
1 CTAAACC
*
2541851 CTAAACT
1 CTAAACC
2541858 CTAAACC
1 CTAAACC
2541865 CTAAA
1 CTAAA
2541870 ACTTAAATCC
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
6 1 0.02
7 52 0.98
ACGTcount: A:0.43, C:0.37, G:0.00, T:0.21
Consensus pattern (7 bp):
CTAAACC
Found at i:2541876 original size:14 final size:14
Alignment explanation
Indices: 2541802--2541947 Score: 78
Period size: 14 Copynumber: 10.4 Consensus size: 14
2541792 AACTTAAATT
*
2541802 CTAAACCCTAAACC
1 CTAAACCCTAAAAC
**
2541816 CTAAACCCTAATCC
1 CTAAACCCTAAAAC
* *
2541830 CTAATCCCTAATAC
1 CTAAACCCTAAAAC
*
2541844 ATAAACCCT-AAAC
1 CTAAACCCTAAAAC
2541857 TCTAAACCCTAAAAC
1 -CTAAACCCTAAAAC
* * **
2541872 TTAAATCCTATCAC
1 CTAAACCCTAAAAC
* * * *
2541886 ATGAACTCTAAATC
1 CTAAACCCTAAAAC
* * **
2541900 CCAAACCTTATCAC
1 CTAAACCCTAAAAC
* * *
2541914 ATAAACTCTAAATC
1 CTAAACCCTAAAAC
*
2541928 CTAAACCCTAAACC
1 CTAAACCCTAAAAC
2541942 CTAAAC
1 CTAAAC
2541948 ATTATCATTA
Statistics
Matches: 94, Mismatches: 36, Indels: 4
0.70 0.27 0.03
Matches are distributed among these distances:
13 3 0.03
14 87 0.93
15 4 0.04
ACGTcount: A:0.42, C:0.34, G:0.01, T:0.23
Consensus pattern (14 bp):
CTAAACCCTAAAAC
Found at i:2541946 original size:28 final size:28
Alignment explanation
Indices: 2541802--2541947 Score: 100
Period size: 28 Copynumber: 5.2 Consensus size: 28
2541792 AACTTAAATT
*
2541802 CTAAACCCTAAACCCTAAACCCTAATCC
1 CTAAACCCTAAATCCTAAACCCTAATCC
* * * *
2541830 CTAATCCCT-AATACATAAACCCTAAACT
1 CTAAACCCTAAAT-CCTAAACCCTAATCC
* * *
2541858 CTAAACCCTAAAACTTAAATCCT-ATCAC
1 CTAAACCCTAAATCCTAAACCCTAATC-C
* * * * *
2541886 ATGAACTCTAAATCCCAAA-CCTTATCAC
1 CTAAACCCTAAATCCTAAACCCTAATC-C
* * *
2541914 ATAAACTCTAAATCCTAAACCCTAAACC
1 CTAAACCCTAAATCCTAAACCCTAATCC
2541942 CTAAAC
1 CTAAAC
2541948 ATTATCATTA
Statistics
Matches: 91, Mismatches: 22, Indels: 10
0.74 0.18 0.08
Matches are distributed among these distances:
27 7 0.08
28 77 0.85
29 7 0.08
ACGTcount: A:0.42, C:0.34, G:0.01, T:0.23
Consensus pattern (28 bp):
CTAAACCCTAAATCCTAAACCCTAATCC
Found at i:2551614 original size:18 final size:19
Alignment explanation
Indices: 2551585--2551621 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
2551575 AGCAGTTAAG
2551585 CTTTCATCTTTCTCTTTTC
1 CTTTCATCTTTCTCTTTTC
*
2551604 CTTTC-TCTTTCTTTTTTC
1 CTTTCATCTTTCTCTTTTC
2551622 TCGTATTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.03, C:0.30, G:0.00, T:0.68
Consensus pattern (19 bp):
CTTTCATCTTTCTCTTTTC
Found at i:2563115 original size:15 final size:15
Alignment explanation
Indices: 2563095--2563137 Score: 77
Period size: 15 Copynumber: 2.8 Consensus size: 15
2563085 ATAGGACTCG
2563095 AACCCGATGGGTTCT
1 AACCCGATGGGTTCT
2563110 AACCCGATGGGTTCT
1 AACCCGATGGGTTCT
2563125 AACCCGATCGGGT
1 AACCCGAT-GGGT
2563138 CGGGTCGAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 23 0.85
16 4 0.15
ACGTcount: A:0.21, C:0.28, G:0.28, T:0.23
Consensus pattern (15 bp):
AACCCGATGGGTTCT
Found at i:2579166 original size:50 final size:50
Alignment explanation
Indices: 2579106--2579211 Score: 212
Period size: 50 Copynumber: 2.1 Consensus size: 50
2579096 GGAAACAACC
2579106 AAACAACTTGGTTCTTTTGTAACTGAGATACTTAGACATGTTAATCAATT
1 AAACAACTTGGTTCTTTTGTAACTGAGATACTTAGACATGTTAATCAATT
2579156 AAACAACTTGGTTCTTTTGTAACTGAGATACTTAGACATGTTAATCAATT
1 AAACAACTTGGTTCTTTTGTAACTGAGATACTTAGACATGTTAATCAATT
2579206 AAACAA
1 AAACAA
2579212 TAAAAGATGG
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 56 1.00
ACGTcount: A:0.37, C:0.14, G:0.13, T:0.36
Consensus pattern (50 bp):
AAACAACTTGGTTCTTTTGTAACTGAGATACTTAGACATGTTAATCAATT
Found at i:2586985 original size:17 final size:17
Alignment explanation
Indices: 2586963--2587004 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
2586953 TACATTAAAA
*
2586963 ATATAAAATAATATTTT
1 ATATAAAATAATATATT
*
2586980 ATATAAAACAATATATT
1 ATATAAAATAATATATT
2586997 -TATAAAAT
1 ATATAAAAT
2587005 TCAATACCCT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
16 7 0.32
17 15 0.68
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (17 bp):
ATATAAAATAATATATT
Found at i:2587009 original size:18 final size:16
Alignment explanation
Indices: 2586964--2587010 Score: 51
Period size: 18 Copynumber: 2.8 Consensus size: 16
2586954 ACATTAAAAA
2586964 TATAAAAT-AATATTT
1 TATAAAATCAATATTT
*
2586979 TATATAAAACAATATATT
1 TATA-AAATCAATAT-TT
2586997 TATAAAATTCAATA
1 TATAAAA-TCAATA
2587011 CCCTAAATCT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
15 4 0.15
16 3 0.12
17 8 0.31
18 11 0.42
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.40
Consensus pattern (16 bp):
TATAAAATCAATATTT
Found at i:2587393 original size:13 final size:13
Alignment explanation
Indices: 2587375--2587401 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2587365 CTCAAACCTT
2587375 TCGTCGTGAATCG
1 TCGTCGTGAATCG
2587388 TCGTCGTGAATCG
1 TCGTCGTGAATCG
2587401 T
1 T
2587402 TAATTTCAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.22, G:0.30, T:0.33
Consensus pattern (13 bp):
TCGTCGTGAATCG
Found at i:2594146 original size:20 final size:20
Alignment explanation
Indices: 2594121--2594158 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2594111 CCCCCTTTGA
*
2594121 AGGGGAACCGATTCCCCCAC
1 AGGGGAACCGATACCCCCAC
*
2594141 AGGGGAATCGATACCCCC
1 AGGGGAACCGATACCCCC
2594159 TGGGGTTCTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.37, G:0.26, T:0.11
Consensus pattern (20 bp):
AGGGGAACCGATACCCCCAC
Found at i:2598190 original size:32 final size:31
Alignment explanation
Indices: 2598114--2598190 Score: 100
Period size: 31 Copynumber: 2.5 Consensus size: 31
2598104 CTAATGTGAC
* *
2598114 TCTTAGGTAGGCTCTGCGGCCCTGAGATCAT
1 TCTTAGGTAGGCCCTGCGGCCCTAAGATCAT
* **
2598145 TCTCAGGTAGGCCCTGCGGCCCTAAGATGTGT
1 TCTTAGGTAGGCCCTGCGGCCCTAAGAT-CAT
2598177 TCTTAGGTAGGCCC
1 TCTTAGGTAGGCCC
2598191 CGAAACTTTC
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
31 25 0.64
32 14 0.36
ACGTcount: A:0.16, C:0.27, G:0.30, T:0.27
Consensus pattern (31 bp):
TCTTAGGTAGGCCCTGCGGCCCTAAGATCAT
Found at i:2601830 original size:31 final size:32
Alignment explanation
Indices: 2601782--2601862 Score: 92
Period size: 32 Copynumber: 2.6 Consensus size: 32
2601772 TGTGACTCTT
* * *
2601782 AGGTAGGCTCCGCGGCCCTGAGAT-CATTCTC
1 AGGTAGGCCCCGTGGCCCTAAGATACATTCTC
* * * *
2601813 GGGTAGGCCCTGTGGCCCTAAGATATATTCTT
1 AGGTAGGCCCCGTGGCCCTAAGATACATTCTC
2601845 AGGTAGGCCCCGTGGCCC
1 AGGTAGGCCCCGTGGCCC
2601863 CGAAACTTTC
Statistics
Matches: 40, Mismatches: 9, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
31 19 0.47
32 21 0.52
ACGTcount: A:0.16, C:0.30, G:0.31, T:0.23
Consensus pattern (32 bp):
AGGTAGGCCCCGTGGCCCTAAGATACATTCTC
Found at i:2601850 original size:32 final size:30
Alignment explanation
Indices: 2601778--2601862 Score: 89
Period size: 31 Copynumber: 2.7 Consensus size: 30
2601768 CTAATGTGAC
* *
2601778 TCTTAGGTAGGCTCCGCGGCCCTGAGATCAT
1 TCTTAGGTAGGC-CCGTGGCCCTAAGATCAT
** *
2601809 TCTCGGGTAGGCCCTGTGGCCCTAAGATATAT
1 TCTTAGGTAGGCCC-GTGGCCCTAAGAT-CAT
2601841 TCTTAGGTAGGCCCCGTGGCCC
1 TCTTAGGTAGG-CCCGTGGCCC
2601863 CGAAACTTTC
Statistics
Matches: 44, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
30 2 0.05
31 21 0.48
32 18 0.41
33 3 0.07
ACGTcount: A:0.15, C:0.29, G:0.29, T:0.26
Consensus pattern (30 bp):
TCTTAGGTAGGCCCGTGGCCCTAAGATCAT
Found at i:2610292 original size:5 final size:5
Alignment explanation
Indices: 2610284--2610324 Score: 82
Period size: 5 Copynumber: 8.2 Consensus size: 5
2610274 CATGAGTTGA
2610284 TGGAG TGGAG TGGAG TGGAG TGGAG TGGAG TGGAG TGGAG T
1 TGGAG TGGAG TGGAG TGGAG TGGAG TGGAG TGGAG TGGAG T
2610325 TTGAGGAGAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 36 1.00
ACGTcount: A:0.20, C:0.00, G:0.59, T:0.22
Consensus pattern (5 bp):
TGGAG
Found at i:2613866 original size:24 final size:24
Alignment explanation
Indices: 2613839--2613884 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
2613829 CTAGAAGGCC
2613839 GGTTGATTTTCAAACTAAGGGGTT
1 GGTTGATTTTCAAACTAAGGGGTT
*
2613863 GGTTGATTTTCAAATTAAGGGG
1 GGTTGATTTTCAAACTAAGGGG
2613885 CTGCTTTGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.26, C:0.07, G:0.30, T:0.37
Consensus pattern (24 bp):
GGTTGATTTTCAAACTAAGGGGTT
Found at i:2621137 original size:22 final size:21
Alignment explanation
Indices: 2621089--2621172 Score: 80
Period size: 21 Copynumber: 3.9 Consensus size: 21
2621079 TTTTGGTGCA
2621089 GAGGGAATCGATTCCTCCCCCT
1 GAGGGAATCGATTCC-CCCCCT
**
2621111 GAGGGAATCGATTCCCCCTTT
1 GAGGGAATCGATTCCCCCCCT
* *
2621132 GAAGGGGAACCGATTCCCCCCACA
1 G-A-GGGAATCGATTCCCCCC-CT
*
2621156 G-GGGAATCGATACCCCC
1 GAGGGAATCGATTCCCCC
2621173 TGGGGATCTG
Statistics
Matches: 51, Mismatches: 8, Indels: 7
0.77 0.12 0.11
Matches are distributed among these distances:
21 19 0.37
22 16 0.31
23 15 0.29
24 1 0.02
ACGTcount: A:0.23, C:0.35, G:0.25, T:0.18
Consensus pattern (21 bp):
GAGGGAATCGATTCCCCCCCT
Found at i:2627993 original size:2 final size:2
Alignment explanation
Indices: 2627986--2628055 Score: 126
Period size: 2 Copynumber: 36.0 Consensus size: 2
2627976 TTAATTGATA
2627986 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2628027 AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2628056 GAATGTGTAA
Statistics
Matches: 66, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
1 2 0.03
2 64 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2631506 original size:34 final size:34
Alignment explanation
Indices: 2631463--2631579 Score: 131
Period size: 34 Copynumber: 3.6 Consensus size: 34
2631453 TTCGTCCTAC
2631463 TAGGATTCAAACTCCTAAAAATATGATAGAATTT
1 TAGGATTCAAACTCCTAAAAATATGATAGAATTT
*
2631497 TAGGATTCAAACTCCTAAAGATATGATAGAATTTT
1 TAGGATTCAAACTCCTAAAAATATGATAGAA-TTT
2631532 GCTAGGATTC--A-----AAAAATATGATAGAATTT
1 --TAGGATTCAAACTCCTAAAAATATGATAGAATTT
* *
2631561 TATGATTTAAACTCCTAAA
1 TAGGATTCAAACTCCTAAA
2631580 GATAGGATCC
Statistics
Matches: 69, Mismatches: 4, Indels: 20
0.74 0.04 0.22
Matches are distributed among these distances:
27 6 0.09
29 4 0.06
30 14 0.20
34 33 0.48
35 4 0.06
37 8 0.12
ACGTcount: A:0.43, C:0.11, G:0.13, T:0.33
Consensus pattern (34 bp):
TAGGATTCAAACTCCTAAAAATATGATAGAATTT
Found at i:2631884 original size:23 final size:22
Alignment explanation
Indices: 2631853--2631914 Score: 58
Period size: 23 Copynumber: 2.8 Consensus size: 22
2631843 CTTTTCTTTT
2631853 TTTTCATGTAATATTTTTTTTAC
1 TTTT-ATGTAATATTTTTTTTAC
*
2631876 ATTTTATGT-ATTTTCTTTTTTAC
1 -TTTTATGTAATATT-TTTTTTAC
2631899 -TTTA-GTATATATTTTT
1 TTTTATGTA-ATATTTTT
2631915 ATTTTTTTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
20 2 0.06
21 7 0.21
22 8 0.24
23 12 0.36
24 4 0.12
ACGTcount: A:0.21, C:0.06, G:0.05, T:0.68
Consensus pattern (22 bp):
TTTTATGTAATATTTTTTTTAC
Found at i:2631911 original size:24 final size:23
Alignment explanation
Indices: 2631868--2631913 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
2631858 ATGTAATATT
*
2631868 TTTTTTACATTTTATGTATTTTC
1 TTTTTTACATTTTATATATTTTC
2631891 TTTTTTAC-TTTAGTATATATTTT
1 TTTTTTACATTT--TATATATTTT
2631914 TATTTTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 3 0.15
23 8 0.40
24 9 0.45
ACGTcount: A:0.20, C:0.07, G:0.04, T:0.70
Consensus pattern (23 bp):
TTTTTTACATTTTATATATTTTC
Found at i:2631998 original size:32 final size:32
Alignment explanation
Indices: 2631961--2632063 Score: 94
Period size: 32 Copynumber: 3.3 Consensus size: 32
2631951 TTATTATCAG
2631961 TTTTATTAATTT-TTATATATATATAT-TTACTT
1 TTTTATT-ATTTATTATATATATATATATTA-TT
*
2631993 TTTTATTTTTTATTATATATATATATATTA-T
1 TTTTATTATTTATTATATATATATATATTATT
* *
2632024 TTTTACTTTTTTATTAT-TAT-TTTAT-TTATT
1 TTTTA-TTATTTATTATATATATATATATTATT
*
2632054 TGTT-TTATTT
1 TTTTATTATTT
2632064 CTATATTTTC
Statistics
Matches: 63, Mismatches: 4, Indels: 12
0.80 0.05 0.15
Matches are distributed among these distances:
28 5 0.08
29 3 0.05
30 8 0.13
31 12 0.19
32 32 0.51
33 3 0.05
ACGTcount: A:0.26, C:0.02, G:0.01, T:0.71
Consensus pattern (32 bp):
TTTTATTATTTATTATATATATATATATTATT
Found at i:2632063 original size:38 final size:39
Alignment explanation
Indices: 2631904--2632044 Score: 111
Period size: 39 Copynumber: 3.8 Consensus size: 39
2631894 TTTACTTTAG
* *
2631904 TATA-TATTTTTA-TTTTTT-TTAGATTA-TATATATAAA
1 TATATTATTTTTACTTTTTTATT-TATTATTATATATATA
* * * * *
2631940 TATATTATTTTT--TATTATCAGTT-TTATTA-ATTTTTA
1 TATATTATTTTTACT-TTTTTATTTATTATTATATATATA
* *
2631976 TATATATATATTTACTTTTTTATTTTTTATTATATATATA
1 TATAT-TATTTTTACTTTTTTATTTATTATTATATATATA
2632016 TATATTATTTTTACTTTTTTA-TTATTATT
1 TATATTATTTTTACTTTTTTATTTATTATT
2632045 TTATTTATTT
Statistics
Matches: 81, Mismatches: 15, Indels: 16
0.72 0.13 0.14
Matches are distributed among these distances:
36 17 0.21
37 18 0.22
38 14 0.17
39 22 0.27
40 10 0.12
ACGTcount: A:0.30, C:0.02, G:0.01, T:0.66
Consensus pattern (39 bp):
TATATTATTTTTACTTTTTTATTTATTATTATATATATA
Found at i:2632072 original size:13 final size:13
Alignment explanation
Indices: 2631972--2632072 Score: 50
Period size: 13 Copynumber: 7.9 Consensus size: 13
2631962 TTTATTAATT
*
2631972 TTTATATATATATA
1 TTTATATAT-TTTA
2631986 TTTACT-T-TTTTA
1 TTTA-TATATTTTA
* *
2631998 TTT-TTTATTATA
1 TTTATATATTTTA
* *
2632010 TATATATATATTA
1 TTTATATATTTTA
* *
2632023 TTTTTACTTTTTTA
1 TTTATA-TATTTTA
2632037 -TTAT-TATTTTA
1 TTTATATATTTTA
* *
2632048 TTTATTTGTTTTA
1 TTTATATATTTTA
*
2632061 TTTCTATATTTT
1 TTTATATATTTT
2632073 CTTTTTCTTT
Statistics
Matches: 64, Mismatches: 16, Indels: 15
0.67 0.17 0.16
Matches are distributed among these distances:
10 1 0.02
11 7 0.11
12 16 0.25
13 29 0.45
14 10 0.16
15 1 0.02
ACGTcount: A:0.26, C:0.03, G:0.01, T:0.70
Consensus pattern (13 bp):
TTTATATATTTTA
Found at i:2636462 original size:182 final size:183
Alignment explanation
Indices: 2636115--2636463 Score: 619
Period size: 182 Copynumber: 1.9 Consensus size: 183
2636105 ATTAAATCCG
*
2636115 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
1 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTAGCTTTATGA
* * *
2636180 ATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCAGTGTTTGCTCCACTGCTT
66 ATAGATTATCTTCAAACCATGACACTGCTCGGACACTTGGCAATTCAGTGTTTGCTCCACTACTT
2636245 TTGTCAGGCCAAAGACTTTGTGATGAGACGAACCCTTCAGTGATTTGTCCCTC
131 TTGTCAGGCCAAAGACTTTGTGATGAGACGAACCCTTCAGTGATTTGTCCCTC
2636298 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTAGCTTTATGA
1 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTAGCTTTATGA
* * *
2636363 ATAGATTA-CTTCAAACCATGACATTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCATTACTT
66 ATAGATTATCTTCAAACCATGACACTGCTCGGACACTTGGCAATTCAGTGTTTGCTCCACTACTT
*
2636427 TTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTT
131 TTGTCAGGCCAAAGACTTTGTGATGAGACGAACCCTT
2636464 TAGTTAAACC
Statistics
Matches: 158, Mismatches: 8, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
182 86 0.54
183 72 0.46
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.30
Consensus pattern (183 bp):
TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTAGCTTTATGA
ATAGATTATCTTCAAACCATGACACTGCTCGGACACTTGGCAATTCAGTGTTTGCTCCACTACTT
TTGTCAGGCCAAAGACTTTGTGATGAGACGAACCCTTCAGTGATTTGTCCCTC
Found at i:2637792 original size:36 final size:36
Alignment explanation
Indices: 2637752--2637822 Score: 108
Period size: 36 Copynumber: 2.0 Consensus size: 36
2637742 CCTTGAAATG
* *
2637752 AATTTTGTCTCTCTTGAGATAGTT-TCCTTGAAACAA
1 AATTTTGTCTCCCTTGAGACAGTTCT-CTTGAAACAA
2637788 AATTTTGTCTCCCTTGAGACAGTTCTCTTGAAACA
1 AATTTTGTCTCCCTTGAGACAGTTCTCTTGAAACA
2637823 TAAACATTGA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
36 31 0.97
37 1 0.03
ACGTcount: A:0.27, C:0.20, G:0.14, T:0.39
Consensus pattern (36 bp):
AATTTTGTCTCCCTTGAGACAGTTCTCTTGAAACAA
Found at i:2637830 original size:100 final size:102
Alignment explanation
Indices: 2637650--2637950 Score: 484
Period size: 100 Copynumber: 3.0 Consensus size: 102
2637640 CTTAAAACAG
* * * * *
2637650 ATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACAGAAAGTTTGTCTCACTTGAGACAGTTTCTC
1 ATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACA-AAATTTTGTCTCCCTTGAGACAGTTTCTC
*
2637715 TTTAAACATAAACATTGAAAACATTTCCCTTGAAATGA
65 TTGAAACATAAACATTGAAAACATTTCCCTTGAAATGA
2637753 ATTTTGTCTCTCTTGAGATAGTTT-CCTTGAAACAAAATTTTGTCTCCCTTGAGACAG-TTCTCT
1 ATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCT
2637816 TGAAACATAAACATTGAAAACATTTCCCTTGAAATGA
66 TGAAACATAAACATTGAAAACATTTCCCTTGAAATGA
*
2637853 ATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAAC-AAATTTTGTCT-CCTTGAGACAGTTTCTAT
1 ATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCT
*
2637916 TGAAACATAAACTTTGAAAACAGTTTCCCTTGAAA
66 TGAAACATAAACATTGAAAACA-TTTCCCTTGAAA
2637951 CAAAATCTTT
Statistics
Matches: 187, Mismatches: 8, Indels: 8
0.92 0.04 0.04
Matches are distributed among these distances:
99 11 0.06
100 103 0.55
101 42 0.22
102 9 0.05
103 22 0.12
ACGTcount: A:0.31, C:0.19, G:0.13, T:0.37
Consensus pattern (102 bp):
ATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCT
TGAAACATAAACATTGAAAACATTTCCCTTGAAATGA
Found at i:2637911 original size:35 final size:35
Alignment explanation
Indices: 2637838--2638086 Score: 140
Period size: 36 Copynumber: 7.4 Consensus size: 35
2637828 ATTGAAAACA
** *
2637838 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAG
1 TTTCCCTTGAAACAAATTTTGTCTC-CTTGAGACAG
2637874 TTTCCCTTGAAACAAATTTTGTCTCCTTGAGACAG
1 TTTCCCTTGAAACAAATTTTGTCTCCTTGAGACAG
** * *
2637909 TTTCTATTGAAACATAA-----ACT--TTGAAAACAG
1 TTTCCCTTGAAACA-AATTTTGTCTCCTTG-AGACAG
* *
2637939 TTTCCCTTGAAACAAA----ATCT--TTGA-ATATG
1 TTTCCCTTGAAACAAATTTTGTCTCCTTGAGACA-G
* * *
2637968 TTTACATT-AAACAAATTTCGTCTCTCTTGAGACAG
1 TTTCCCTTGAAACAAATTTTGTCTC-CTTGAGACAG
*
2638003 TTT-CC-TGAAACAAA-TTTGTCTCTCTTAAGACATG
1 TTTCCCTTGAAACAAATTTTGTCTC-CTTGAGACA-G
* *
2638037 TTT-TCTTAAAACAAAATTTTGTCTCCCTTGAGACAG
1 TTTCCCTTGAAAC-AAATTTTGTCT-CCTTGAGACAG
*
2638073 TTTCTCTTGAAACA
1 TTTCCCTTGAAACA
2638087 TCAATCCTTG
Statistics
Matches: 172, Mismatches: 22, Indels: 38
0.74 0.09 0.16
Matches are distributed among these distances:
28 9 0.05
29 13 0.08
30 22 0.13
31 2 0.01
32 3 0.02
33 17 0.10
34 13 0.08
35 34 0.20
36 35 0.20
37 23 0.13
38 1 0.01
ACGTcount: A:0.31, C:0.19, G:0.12, T:0.39
Consensus pattern (35 bp):
TTTCCCTTGAAACAAATTTTGTCTCCTTGAGACAG
Found at i:2637939 original size:30 final size:30
Alignment explanation
Indices: 2637905--2637963 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
2637895 TCTCCTTGAG
*
2637905 ACAGTTTCTATTGAAACATAAA-CTTTGAAA
1 ACAGTTTCCATTGAAACA-AAATCTTTGAAA
*
2637935 ACAGTTTCCCTTGAAACAAAATCTTTGAA
1 ACAGTTTCCATTGAAACAAAATCTTTGAA
2637964 TATGTTTACA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 3 0.12
30 23 0.88
ACGTcount: A:0.41, C:0.17, G:0.10, T:0.32
Consensus pattern (30 bp):
ACAGTTTCCATTGAAACAAAATCTTTGAAA
Found at i:2638061 original size:37 final size:35
Alignment explanation
Indices: 2637976--2638086 Score: 136
Period size: 37 Copynumber: 3.1 Consensus size: 35
2637966 TGTTTACATT
* *
2637976 AAACAAATTTCGTCTCTCTTGAGACAG-TTTCCTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTTCTTG
* *
2638010 AAACAAA-TTTGTCTCTCTTAAGACATGTTTTCTTA
1 AAACAAATTTTGTCTCTCTTGAGACA-GTTTTCTTG
*
2638045 AAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTG
1 AAAC-AAATTTTGTCTCTCTTGAGACAGTTT-TCTTG
2638082 AAACA
1 AAACA
2638087 TCAATCCTTG
Statistics
Matches: 65, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
33 16 0.25
34 8 0.12
35 9 0.14
36 8 0.12
37 24 0.37
ACGTcount: A:0.31, C:0.21, G:0.12, T:0.37
Consensus pattern (35 bp):
AAACAAATTTTGTCTCTCTTGAGACAGTTTTCTTG
Found at i:2638188 original size:33 final size:33
Alignment explanation
Indices: 2638124--2638238 Score: 162
Period size: 33 Copynumber: 3.5 Consensus size: 33
2638114 CCATGATACA
2638124 GTTTCTCTTGAAACACAAAAAGAAACCTTTGAAATT
1 GTTTCTCTTGAAACAC--AAA-AAACCTTTGAAATT
*
2638160 GTTTCTCTTGAAACACAAAAAACCTTTGAAAAT
1 GTTTCTCTTGAAACACAAAAAACCTTTGAAATT
*
2638193 GTTTCTCTTGAAACAC--AAAACCTTTGAGATT
1 GTTTCTCTTGAAACACAAAAAACCTTTGAAATT
*
2638224 GTTTCCCTTGAAACA
1 GTTTCTCTTGAAACA
2638239 AATTTCGTCT
Statistics
Matches: 75, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
31 27 0.36
33 29 0.39
34 3 0.04
36 16 0.21
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.32
Consensus pattern (33 bp):
GTTTCTCTTGAAACACAAAAAACCTTTGAAATT
Found at i:2638285 original size:67 final size:66
Alignment explanation
Indices: 2638193--2638374 Score: 240
Period size: 67 Copynumber: 2.8 Consensus size: 66
2638183 CTTTGAAAAT
*
2638193 GTTTCTCTTGAAACACAAAACCTTTGAGATTGTTTCCCTTGAAACAAATTTCGTCTCCCTTGAGA
1 GTTTCTCTTGAAACACAAAATCTTTGAGATTGTTTCCCTTGAAACAAATTTCGTCT-CCTTGAGA
2638258 CA
65 CA
* * * * *
2638260 GTTTCTCTTGAAACACAAAATCTTTGAGTTTATTTCCCTTAAAACAAATTTTGTCTCCTTGAGGC
1 GTTTCTCTTGAAACACAAAATCTTTGAGATTGTTTCCCTTGAAACAAATTTCGTCTCCTTGAGAC
*
2638325 C
66 A
* * * * *
2638326 GTTTCTCATGAAACA-TATATCTTTAAGATTGTTTCCCTTGAAACGAATT
1 GTTTCTCTTGAAACACAAAATCTTTGAGATTGTTTCCCTTGAAACAAATT
2638375 CTGTCTTTTT
Statistics
Matches: 100, Mismatches: 15, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
65 27 0.27
66 22 0.22
67 51 0.51
ACGTcount: A:0.29, C:0.21, G:0.13, T:0.38
Consensus pattern (66 bp):
GTTTCTCTTGAAACACAAAATCTTTGAGATTGTTTCCCTTGAAACAAATTTCGTCTCCTTGAGAC
A
Done.