Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010176.1 Kokia drynarioides strain JFW-HI SEQ_124981, 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: 93874
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 4 characters in sequence are not A, C, G, or T
Found at i:56 original size:12 final size:11
Alignment explanation
Indices: 37--83 Score: 60
Period size: 11 Copynumber: 4.3 Consensus size: 11
27 AAATACGCAT
37 AAAAACATTAA
1 AAAAACATTAA
48 AACAAACATTAA
1 AA-AAACATTAA
60 AAAAA-ATTAA
1 AAAAACATTAA
**
70 AAATTCATTAA
1 AAAAACATTAA
81 AAA
1 AAA
84 TATTTATATT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
10 8 0.25
11 13 0.41
12 11 0.34
ACGTcount: A:0.70, C:0.09, G:0.00, T:0.21
Consensus pattern (11 bp):
AAAAACATTAA
Found at i:552 original size:12 final size:11
Alignment explanation
Indices: 533--579 Score: 60
Period size: 11 Copynumber: 4.3 Consensus size: 11
523 AAATACGCAT
533 AAAAACATTAA
1 AAAAACATTAA
544 AACAAACATTAA
1 AA-AAACATTAA
556 AAAAA-ATTAA
1 AAAAACATTAA
**
566 AAATTCATTAA
1 AAAAACATTAA
577 AAA
1 AAA
580 TCTTTATATT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
10 8 0.25
11 13 0.41
12 11 0.34
ACGTcount: A:0.70, C:0.09, G:0.00, T:0.21
Consensus pattern (11 bp):
AAAAACATTAA
Found at i:731 original size:21 final size:22
Alignment explanation
Indices: 684--777 Score: 68
Period size: 23 Copynumber: 4.2 Consensus size: 22
674 AAACAATAGT
*
684 AAAAACACATAAAAATAACATC
1 AAAAACACATAAAAATAACAAC
* *
706 -TAAACA-ATCAAAATAACAAC
1 AAAAACACATAAAAATAACAAC
*
726 AAAAACAGCA-ATAAAACAACAAC
1 AAAAACA-CATA-AAAATAACAAC
* * *
749 AAAAATAGCAACAAAAATAACAAA
1 AAAAACA-C-ATAAAAATAACAAC
773 AAAAA
1 AAAAA
778 TAGTAACAAA
Statistics
Matches: 57, Mismatches: 9, Indels: 10
0.75 0.12 0.13
Matches are distributed among these distances:
20 12 0.21
21 10 0.18
23 19 0.33
24 15 0.26
25 1 0.02
ACGTcount: A:0.71, C:0.17, G:0.02, T:0.10
Consensus pattern (22 bp):
AAAAACACATAAAAATAACAAC
Found at i:746 original size:23 final size:23
Alignment explanation
Indices: 710--764 Score: 74
Period size: 23 Copynumber: 2.3 Consensus size: 23
700 AACATCTAAA
*
710 CAATCAAAATAACAACAAAAACAG
1 CAAT-AAAACAACAACAAAAACAG
*
734 CAATAAAACAACAACAAAAATAG
1 CAATAAAACAACAACAAAAACAG
*
757 CAACAAAA
1 CAATAAAA
765 ATAACAAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
23 24 0.86
24 4 0.14
ACGTcount: A:0.69, C:0.20, G:0.04, T:0.07
Consensus pattern (23 bp):
CAATAAAACAACAACAAAAACAG
Found at i:775 original size:23 final size:24
Alignment explanation
Indices: 715--800 Score: 102
Period size: 24 Copynumber: 3.6 Consensus size: 24
705 CTAAACAATC
* *
715 AAAATAACAACAAAAACAGCAA-T
1 AAAATAACAACAAAAATAGCAACA
*
738 AAAACAACAACAAAAATAGCAACA
1 AAAATAACAACAAAAATAGCAACA
* *
762 AAAATAACAAAAAAAATAGTAACA
1 AAAATAACAACAAAAATAGCAACA
**
786 AAAATATTAACAAAA
1 AAAATAACAACAAAA
801 CAACATCAAA
Statistics
Matches: 53, Mismatches: 9, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
23 20 0.38
24 33 0.62
ACGTcount: A:0.72, C:0.14, G:0.03, T:0.10
Consensus pattern (24 bp):
AAAATAACAACAAAAATAGCAACA
Found at i:800 original size:11 final size:12
Alignment explanation
Indices: 746--800 Score: 65
Period size: 12 Copynumber: 4.6 Consensus size: 12
736 ATAAAACAAC
*
746 AACAAAAATAGC
1 AACAAAAATAGT
**
758 AACAAAAATAAC
1 AACAAAAATAGT
*
770 AAAAAAAATAGT
1 AACAAAAATAGT
*
782 AACAAAAATATT
1 AACAAAAATAGT
794 AACAAAA
1 AACAAAA
801 CAACATCAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 37 1.00
ACGTcount: A:0.73, C:0.11, G:0.04, T:0.13
Consensus pattern (12 bp):
AACAAAAATAGT
Found at i:800 original size:12 final size:12
Alignment explanation
Indices: 715--791 Score: 77
Period size: 12 Copynumber: 6.5 Consensus size: 12
705 CTAAACAATC
*
715 AAAATAACAACA
1 AAAATAGCAACA
* *
727 AAAACAGCAATA
1 AAAATAGCAACA
739 AAACA-A-CAACA
1 AAA-ATAGCAACA
750 AAAATAGCAACA
1 AAAATAGCAACA
* *
762 AAAATAACAAAA
1 AAAATAGCAACA
*
774 AAAATAGTAACA
1 AAAATAGCAACA
786 AAAATA
1 AAAATA
792 TTAACAAAAC
Statistics
Matches: 53, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
10 1 0.02
11 8 0.15
12 43 0.81
13 1 0.02
ACGTcount: A:0.73, C:0.14, G:0.04, T:0.09
Consensus pattern (12 bp):
AAAATAGCAACA
Found at i:863 original size:12 final size:12
Alignment explanation
Indices: 715--868 Score: 52
Period size: 12 Copynumber: 12.8 Consensus size: 12
705 CTAAACAATC
*
715 AAAATAACAACA
1 AAAATAACAAAA
* * *
727 AAAACAGC-AAT
1 AAAATAACAAAA
* *
738 AAAACAACAACA
1 AAAATAACAAAA
* *
750 AAAATAGCAACA
1 AAAATAACAAAA
762 AAAATAACAAAAA
1 AAAATAAC-AAAA
775 AAATAGTAACAAAA
1 AAA-A-TAACAAAA
* *
789 ATATTAACAAAA
1 AAAATAACAAAA
*
801 CAACAT--C-AAA
1 -AAAATAACAAAA
*
811 ACAATAA-AAAA
1 AAAATAACAAAA
822 ATACCAA-AACAATAA
1 A-A--AATAACAA-AA
**
837 AAAATAAC-ATC
1 AAAATAACAAAA
848 AAAATAACAAAA
1 AAAATAACAAAA
*
860 AAAAAAACA
1 AAAATAACA
869 GTAACCAAAA
Statistics
Matches: 103, Mismatches: 24, Indels: 30
0.66 0.15 0.19
Matches are distributed among these distances:
9 3 0.03
10 3 0.03
11 21 0.20
12 44 0.43
13 13 0.13
14 12 0.12
15 7 0.07
ACGTcount: A:0.73, C:0.15, G:0.02, T:0.10
Consensus pattern (12 bp):
AAAATAACAAAA
Found at i:880 original size:24 final size:24
Alignment explanation
Indices: 824--889 Score: 57
Period size: 24 Copynumber: 2.8 Consensus size: 24
814 ATAAAAAAAT
*
824 ACCAAAACAATAAAAAATAACATCA
1 ACCAAAACAA-AAAAAAAAACATCA
849 A--AATAACAAAAAAAAAAACAGT-A
1 ACCAA-AACAAAAAAAAAAACA-TCA
**
872 ACCAAAACAGTAAAAAAA
1 ACCAAAACAAAAAAAAAA
890 CAGCACCAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 9
0.74 0.07 0.20
Matches are distributed among these distances:
23 14 0.41
24 17 0.50
25 3 0.09
ACGTcount: A:0.73, C:0.15, G:0.03, T:0.09
Consensus pattern (24 bp):
ACCAAAACAAAAAAAAAAACATCA
Found at i:1137 original size:256 final size:254
Alignment explanation
Indices: 842--1351 Score: 921
Period size: 256 Copynumber: 2.0 Consensus size: 254
832 AATAAAAAAT
*
842 AACATCAAAATAACAAAAAAAAAAACAGTAACCAAAACAGTAAAAAAACAGCACCAAAAATAACA
1 AACATCAAAATAACAAAAAAAAAAAAAGTAACCAAAACAGTAAAAAAACAGCACCAAAAATAACA
907 ATATAAATTTTTTTTAAAAATGATTAATTTATTCGGGCCGGACCGGATCGAGAATGAGATAAAAA
66 ATATAAATTTTTTTTAAAAATGATTAATTTATTCGGGCCGGACCGGATCGAGAATGAGATAAAAA
* * **
972 ACTCTTACACGAGGCTCGGCTCGTTTAAAAAATATATCTCATTTTTTATCCAAATCCATTTTTCA
131 ACTCTTACACGAAGCTCGGCTCGTTTAAAAAATATATCTAATTTTTTATCCAAATCCATTTACCA
*
1037 TATTTATATTTTTATTCAAATACTTTCATTTTTTTAACGAGCTTTCAAGTTGAATCGAA
196 TACTTATATTTTTATTCAAATACTTTCATTTTTTTAACGAGCTTTCAAGTTGAATCGAA
1096 NAACATCAAAATAACAAAAAAAAAAAAAAGTAACCAAAACAGTAAAAAAACAGCACCAAAAATAA
1 -AACATCAAAATAAC-AAAAAAAAAAAAAGTAACCAAAACAGTAAAAAAACAGCACCAAAAATAA
*
1161 CAATATAATTTTTTTTTAAAAATGATTAATTTATTCGGGCCGGACCGGATCGAGAATGAGATAAA
64 CAATATAAATTTTTTTTAAAAATGATTAATTTATTCGGGCCGGACCGGATCGAGAATGAGATAAA
* *
1226 AAACTCTTACACGAAGTTCGGCTCGTTTAAAAAATATATCTAATTTTTTATCCAAATTCATTTAC
129 AAACTCTTACACGAAGCTCGGCTCGTTTAAAAAATATATCTAATTTTTTATCCAAATCCATTTAC
1291 CATACTTATATTTTTATTCAAATACTTTCATTTTTTTAACGAGCTTTCAAGTTGAATCGAA
194 CATACTTATATTTTTATTCAAATACTTTCATTTTTTTAACGAGCTTTCAAGTTGAATCGAA
1352 TGATCCGGAT
Statistics
Matches: 245, Mismatches: 9, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
255 14 0.06
256 231 0.94
ACGTcount: A:0.43, C:0.15, G:0.10, T:0.31
Consensus pattern (254 bp):
AACATCAAAATAACAAAAAAAAAAAAAGTAACCAAAACAGTAAAAAAACAGCACCAAAAATAACA
ATATAAATTTTTTTTAAAAATGATTAATTTATTCGGGCCGGACCGGATCGAGAATGAGATAAAAA
ACTCTTACACGAAGCTCGGCTCGTTTAAAAAATATATCTAATTTTTTATCCAAATCCATTTACCA
TACTTATATTTTTATTCAAATACTTTCATTTTTTTAACGAGCTTTCAAGTTGAATCGAA
Found at i:1778 original size:22 final size:22
Alignment explanation
Indices: 1738--1779 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
1728 AGTTCTTATA
*
1738 TTTTTATTTTAAATTTTTAATT
1 TTTTTATTTTAAATATTTAATT
1760 TTTTTACTTTTAAA-ATTTAA
1 TTTTTA-TTTTAAATATTTAA
1780 AATTTAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (22 bp):
TTTTTATTTTAAATATTTAATT
Found at i:18080 original size:6 final size:6
Alignment explanation
Indices: 18069--18096 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
18059 CTTGTAATGA
18069 TCCATC TCCATC TCCATC TCCATC TCCA
1 TCCATC TCCATC TCCATC TCCATC TCCA
18097 GGACAGTTCC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.18, C:0.50, G:0.00, T:0.32
Consensus pattern (6 bp):
TCCATC
Found at i:19418 original size:30 final size:30
Alignment explanation
Indices: 19382--19438 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
19372 AAGTTGTTTC
*
19382 TTGCTGCTGCTG-TGGCTGCTGTTGTTGTAA
1 TTGCTGCTGCTGCT-GCAGCTGTTGTTGTAA
19412 TTGCTGCTGCTGCTGCAGCTGTTGTTG
1 TTGCTGCTGCTGCTGCAGCTGTTGTTG
19439 CTGATGATGC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
30 24 0.96
31 1 0.04
ACGTcount: A:0.05, C:0.19, G:0.33, T:0.42
Consensus pattern (30 bp):
TTGCTGCTGCTGCTGCAGCTGTTGTTGTAA
Found at i:19419 original size:3 final size:3
Alignment explanation
Indices: 19413--19564 Score: 52
Period size: 3 Copynumber: 50.7 Consensus size: 3
19403 TTGTTGTAAT
* * * * * ** *
19413 TGC TGC TGC TGC TGC AGC TGT TGT TGC TGA TGA TGC AAC TGC TGT TGC
1 TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC
** ** * * * *** **
19461 AAC TGC AAC TGT TGC TGT TGT TGC TGC TGC TGC TGC AAT TGC AAC TGC
1 TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC
* * *** ** *
19509 TGC TGC TGT TGT TGC TGC TGC TGC AAT TGC AAC TGC TGC TGT TGC TGC
1 TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC
19557 TGC TGC TG
1 TGC TGC TG
19565 GTTCATGTAA
Statistics
Matches: 101, Mismatches: 48, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
3 101 1.00
ACGTcount: A:0.11, C:0.24, G:0.29, T:0.36
Consensus pattern (3 bp):
TGC
Found at i:19474 original size:36 final size:36
Alignment explanation
Indices: 19437--19564 Score: 157
Period size: 36 Copynumber: 3.6 Consensus size: 36
19427 CAGCTGTTGT
* ** * * *
19437 TGCTGATGATGCAACTGCTGTTGCAACTGCAACTGT
1 TGCTGATGTTGCTGCTGCTGCTGCAATTGCAACTGC
*
19473 TGCTGTTGTTGCTGCTGCTGCTGCAATTGCAACTGC
1 TGCTGATGTTGCTGCTGCTGCTGCAATTGCAACTGC
* *
19509 TGCTGCTGTTGTTGCTGCTGCTGCAATTGCAACTGC
1 TGCTGATGTTGCTGCTGCTGCTGCAATTGCAACTGC
* *
19545 TGCTGTTGCTGCTGCTGCTG
1 TGCTGATGTTGCTGCTGCTG
19565 GTTCATGTAA
Statistics
Matches: 80, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
36 80 1.00
ACGTcount: A:0.12, C:0.24, G:0.28, T:0.35
Consensus pattern (36 bp):
TGCTGATGTTGCTGCTGCTGCTGCAATTGCAACTGC
Found at i:19524 original size:15 final size:15
Alignment explanation
Indices: 19506--19564 Score: 73
Period size: 15 Copynumber: 3.9 Consensus size: 15
19496 CAATTGCAAC
*
19506 TGCTGCTGCTGTTGT
1 TGCTGCTGCTGCTGT
**
19521 TGCTGCTGCTGCAAT
1 TGCTGCTGCTGCTGT
**
19536 TGCAACTGCTGCTGT
1 TGCTGCTGCTGCTGT
19551 TGCTGCTGCTGCTG
1 TGCTGCTGCTGCTG
19565 GTTCATGTAA
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
15 35 1.00
ACGTcount: A:0.07, C:0.25, G:0.31, T:0.37
Consensus pattern (15 bp):
TGCTGCTGCTGCTGT
Found at i:20096 original size:18 final size:18
Alignment explanation
Indices: 20055--20096 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
20045 CTGCTGTGGT
*
20055 TGTTGCTGCTGCTGCTGC
1 TGTTGCCGCTGCTGCTGC
**
20073 AATTGCCGCTGCTGCTGC
1 TGTTGCCGCTGCTGCTGC
20091 TGTTGC
1 TGTTGC
20097 ATCATCTGAA
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.05, C:0.29, G:0.31, T:0.36
Consensus pattern (18 bp):
TGTTGCCGCTGCTGCTGC
Found at i:28959 original size:31 final size:31
Alignment explanation
Indices: 28924--28988 Score: 121
Period size: 31 Copynumber: 2.1 Consensus size: 31
28914 TGGTTGTTTA
*
28924 TCACTTTTTGATAACGTTAATGACTGTTTTG
1 TCACTTTTCGATAACGTTAATGACTGTTTTG
28955 TCACTTTTCGATAACGTTAATGACTGTTTTG
1 TCACTTTTCGATAACGTTAATGACTGTTTTG
28986 TCA
1 TCA
28989 TATTTTCAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.23, C:0.15, G:0.15, T:0.46
Consensus pattern (31 bp):
TCACTTTTCGATAACGTTAATGACTGTTTTG
Found at i:40935 original size:25 final size:25
Alignment explanation
Indices: 40894--40945 Score: 61
Period size: 24 Copynumber: 2.1 Consensus size: 25
40884 TTATTCTTTT
*
40894 AAAAAGATTTTGTTA-TTATTTAAA
1 AAAAAGATTTTGATATTTATTTAAA
* *
40918 AAAAATATTTTCGATATTTATTTTAA
1 AAAAAGATTTT-GATATTTATTTAAA
40944 AA
1 AA
40946 TATTTTTATT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 10 0.43
25 3 0.13
26 10 0.43
ACGTcount: A:0.46, C:0.02, G:0.06, T:0.46
Consensus pattern (25 bp):
AAAAAGATTTTGATATTTATTTAAA
Found at i:48056 original size:18 final size:17
Alignment explanation
Indices: 48022--48073 Score: 54
Period size: 18 Copynumber: 3.1 Consensus size: 17
48012 ATAATATAAA
*
48022 TAATAAATAATTATTATT
1 TAATTAATAA-TATTATT
*
48040 TATTATAATAATATTA-T
1 TAAT-TAATAATATTATT
48057 TAATTAAT-ATATTATT
1 TAATTAATAATATTATT
48073 T
1 T
48074 GAAAACATAA
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
15 6 0.21
16 6 0.21
17 4 0.14
18 8 0.28
19 5 0.17
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
TAATTAATAATATTATT
Found at i:48057 original size:21 final size:23
Alignment explanation
Indices: 48013--48067 Score: 62
Period size: 21 Copynumber: 2.5 Consensus size: 23
48003 TTATATTTTA
48013 TAATATAA-ATAATAAATAATTAT
1 TAAT-TAATATAATAAATAATTAT
* *
48036 TATTTATTATAAT-AAT-ATTAT
1 TAATTAATATAATAAATAATTAT
48057 TAATTAATATA
1 TAATTAATATA
48068 TTATTTGAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
21 14 0.52
22 5 0.19
23 8 0.30
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (23 bp):
TAATTAATATAATAAATAATTAT
Found at i:56118 original size:16 final size:17
Alignment explanation
Indices: 56093--56125 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
56083 AATTAATTCA
56093 ATTTTCTTATAATTTAT
1 ATTTTCTTATAATTTAT
*
56110 ATTTT-TTATGATTTAT
1 ATTTTCTTATAATTTAT
56126 TAATAATAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.27, C:0.03, G:0.03, T:0.67
Consensus pattern (17 bp):
ATTTTCTTATAATTTAT
Found at i:67691 original size:14 final size:14
Alignment explanation
Indices: 67672--67699 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
67662 ATTCTAAAAA
67672 TTTTAAAAATTTTT
1 TTTTAAAAATTTTT
67686 TTTTAAAAATTTTT
1 TTTTAAAAATTTTT
67700 AACATTTTTT
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:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (14 bp):
TTTTAAAAATTTTT
Found at i:67696 original size:23 final size:23
Alignment explanation
Indices: 67666--67710 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
67656 CATCTAATTC
67666 TAAAAATTTTAAAAATTTTTTTT
1 TAAAAATTTTAAAAATTTTTTTT
* *
67689 TAAAAATTTTTAACATTTTTTT
1 TAAAAATTTTAAAAATTTTTTT
67711 AATGTAACTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (23 bp):
TAAAAATTTTAAAAATTTTTTTT
Found at i:79131 original size:23 final size:22
Alignment explanation
Indices: 79089--79131 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
79079 CATCGACTAC
*
79089 ACCTTTTTTTTCCCCTCTTTTG
1 ACCTTTTTTTTCCCCACTTTTG
79111 ACCTTTTTTTTCCCCAACTTT
1 ACCTTTTTTTTCCCC-ACTTT
79132 CTTTCTGATG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.09, C:0.33, G:0.02, T:0.56
Consensus pattern (22 bp):
ACCTTTTTTTTCCCCACTTTTG
Found at i:91931 original size:4 final size:4
Alignment explanation
Indices: 91922--91952 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
91912 ATAAACGAAA
91922 AGGG AGGG AGGG AGGG AGGG AGGG AGGG AGG
1 AGGG AGGG AGGG AGGG AGGG AGGG AGGG AGG
91953 CAAAGCCCTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.26, C:0.00, G:0.74, T:0.00
Consensus pattern (4 bp):
AGGG
Found at i:93555 original size:2 final size:2
Alignment explanation
Indices: 93548--93580 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
93538 TTAAGTTTTA
93548 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
93581 TTTTTCCATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Done.