Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168010.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_265, 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: 41048
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Found at i:1476 original size:62 final size:59
Alignment explanation
Indices: 1381--1500 Score: 143
Period size: 62 Copynumber: 2.0 Consensus size: 59
1371 GGCTTTTCTA
* *
1381 GCCAAAAATGACTTGAATAATCCCCTTAAATTTTTATGAGTGGATTATTGA-AGATGTTTTTG
1 GCCAAAAATGACTTCAATAATCCCCTCAAATTTTT-T--GTGGATTATTGATAG-TGTTTTTG
* ** *
1443 GCCAAAAATGCCTTCAATAATCCCCTCCCATTTTTTTTGGATTATTGATAGTGTTTTT
1 GCCAAAAATGACTTCAATAATCCCCTCAAATTTTTTGTGGATTATTGATAGTGTTTTT
1501 TTTTTTTTTG
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
59 18 0.35
60 2 0.04
61 1 0.02
62 30 0.59
ACGTcount: A:0.28, C:0.16, G:0.15, T:0.41
Consensus pattern (59 bp):
GCCAAAAATGACTTCAATAATCCCCTCAAATTTTTTGTGGATTATTGATAGTGTTTTTG
Found at i:1704 original size:64 final size:62
Alignment explanation
Indices: 1513--1704 Score: 163
Period size: 64 Copynumber: 3.0 Consensus size: 62
1503 TTTTTTTGAG
* * * * * * * * *
1513 AAAATGCCTTGAATAATCCCATAGAAAAAATTGAATGGGGTTAGTCAAGGCGTTTATGAC-CA
1 AAAATACCTTGAATAATCCCTTACAAAATATTAAAT-GGGTTATTGAAGGCGTTTTTGACAAA
** * * * *
1575 AAAATACCTTGAATAATCCCTT-TTAATTTTTATAATGGGATTATTGAAGGCATTTTTAGCCAAA
1 AAAATACCTTGAATAATCCCTTACAAAATATTA-AATGGG-TTATTGAAGGCGTTTTT-GACAAA
* * *
1639 AAAATATCTTGAATAATCCCTTACAAAATATTAAATAGGGTTATTGAAGGTGTTTTTGACTAA
1 AAAATACCTTGAATAATCCCTTACAAAATATTAAAT-GGGTTATTGAAGGCGTTTTTGACAAA
1702 AAA
1 AAA
1705 CGTCTTTAAT
Statistics
Matches: 101, Mismatches: 23, Indels: 11
0.75 0.17 0.08
Matches are distributed among these distances:
61 7 0.07
62 36 0.36
63 9 0.09
64 40 0.40
65 9 0.09
ACGTcount: A:0.39, C:0.12, G:0.16, T:0.33
Consensus pattern (62 bp):
AAAATACCTTGAATAATCCCTTACAAAATATTAAATGGGTTATTGAAGGCGTTTTTGACAAA
Found at i:2993 original size:22 final size:22
Alignment explanation
Indices: 2965--3055 Score: 80
Period size: 22 Copynumber: 4.2 Consensus size: 22
2955 TAATTTACTT
2965 ATAAATAATATTATATTAATAA
1 ATAAATAATATTATATTAATAA
* *
2987 ATAAATACTATTA-ATATAATAT
1 ATAAATAATATTATAT-TAATAA
* *
3009 ATTAATAA-A-AATATTAATAA
1 ATAAATAATATTATATTAATAA
* * *
3029 ATAATATTATAATATATTCATAA
1 ATAA-ATAATATTATATTAATAA
3052 ATAA
1 ATAA
3056 TATTGTATTT
Statistics
Matches: 54, Mismatches: 10, Indels: 9
0.74 0.14 0.12
Matches are distributed among these distances:
20 9 0.17
21 8 0.15
22 24 0.44
23 13 0.24
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (22 bp):
ATAAATAATATTATATTAATAA
Found at i:3023 original size:25 final size:26
Alignment explanation
Indices: 2968--3059 Score: 77
Period size: 23 Copynumber: 3.5 Consensus size: 26
2958 TTTACTTATA
*
2968 AATAATATTATATTAATAAATAAATACTATT
1 AATAA-ATAATATTAATAAAT--A-A-TATT
2999 AATATAAT-ATATTAATAAA-AATATT
1 AATA-AATAATATTAATAAATAATATT
3024 AATAAATAATATT-AT-AAT-ATATT
1 AATAAATAATATTAATAAATAATATT
*
3047 CATAAATAATATT
1 AATAAATAATATT
3060 GTATTTGAAG
Statistics
Matches: 57, Mismatches: 1, Indels: 14
0.79 0.01 0.19
Matches are distributed among these distances:
23 19 0.33
24 5 0.09
25 13 0.23
26 1 0.02
27 1 0.02
30 11 0.19
31 6 0.11
32 1 0.02
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (26 bp):
AATAAATAATATTAATAAATAATATT
Found at i:3045 original size:23 final size:25
Alignment explanation
Indices: 2986--3059 Score: 91
Period size: 23 Copynumber: 3.0 Consensus size: 25
2976 TATATTAATA
2986 AATAAATACTATTAATATAAT-ATATT
1 AATAAATA-TATTAATA-AATAATATT
*
3012 AATAAAAATATTAATAAATAATATT
1 AATAAATATATTAATAAATAATATT
*
3037 -AT-AATATATTCATAAATAATATT
1 AATAAATATATTAATAAATAATATT
3060 GTATTTGAAG
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
23 19 0.43
24 5 0.11
25 13 0.30
26 7 0.16
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.41
Consensus pattern (25 bp):
AATAAATATATTAATAAATAATATT
Found at i:13518 original size:2 final size:2
Alignment explanation
Indices: 13511--13535 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
13501 GAGTACAAGA
13511 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
13536 GCTAAAGCAT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:13752 original size:18 final size:18
Alignment explanation
Indices: 13729--13874 Score: 119
Period size: 18 Copynumber: 8.1 Consensus size: 18
13719 AATTTTTTAC
*
13729 AATATTAACAAATAATAT
1 AATATTAATAAATAATAT
13747 AATATTAATAAATAATATTAT
1 AATATTAATAAAT-A-A-TAT
13768 AATATATTAATAAATAATAT
1 -A-ATATTAATAAATAATAT
*
13788 ATTATTAATAAATAATAT
1 AATATTAATAAATAATAT
*
13806 ACTATTAAT--AT-A-AT
1 AATATTAATAAATAATAT
*
13820 -ATATTAATAAATATTATT
1 AATATTAATAAATAATA-T
*
13838 AATA--AAT-AATATTAT
1 AATATTAATAAATAATAT
13853 ACTATATTAATAAATAATAT
1 A--ATATTAATAAATAATAT
13873 AA
1 AA
13875 AGAATAATAA
Statistics
Matches: 106, Mismatches: 6, Indels: 32
0.74 0.04 0.22
Matches are distributed among these distances:
13 7 0.07
14 2 0.02
15 5 0.05
16 9 0.08
17 7 0.07
18 38 0.36
19 8 0.08
20 12 0.11
21 4 0.04
22 2 0.02
23 12 0.11
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (18 bp):
AATATTAATAAATAATAT
Found at i:13778 original size:23 final size:23
Alignment explanation
Indices: 13748--13838 Score: 87
Period size: 23 Copynumber: 3.8 Consensus size: 23
13738 AAATAATATA
13748 ATATTAATAAATAATATTATAAT
1 ATATTAATAAATAATATTATAAT
*
13771 ATATTAATAAATAATA-TATTAT
1 ATATTAATAAATAATATTATAAT
* *
13793 -TAATAAATAATATACTATTAATATAAT
1 AT-ATTAATAA-ATAATATT-ATA--AT
*
13820 ATATTAATAAATATTATTA
1 ATATTAATAAATAATATTA
13839 ATAAATAATA
Statistics
Matches: 55, Mismatches: 6, Indels: 12
0.75 0.08 0.16
Matches are distributed among these distances:
21 1 0.02
22 12 0.22
23 21 0.38
24 1 0.02
25 3 0.05
26 7 0.13
27 9 0.16
28 1 0.02
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (23 bp):
ATATTAATAAATAATATTATAAT
Found at i:13784 original size:41 final size:41
Alignment explanation
Indices: 13730--13874 Score: 193
Period size: 41 Copynumber: 3.5 Consensus size: 41
13720 ATTTTTTACA
*
13730 ATATTAACAAATAATATAATATTAATAAATAATATTATAAT
1 ATATTAATAAATAATATAATATTAATAAATAATATTATAAT
*
13771 ATATTAATAAATAATATATTATTAATAAATAATATACTATTAAT
1 ATATTAATAAATAATATAATATTAATAAATAATAT--TA-TAAT
* * * *
13815 ATAATATATTAATAA-ATATTATTAATAAATAATATTATACT
1 ATATTA-ATAAATAATATAATATTAATAAATAATATTATAAT
13856 ATATTAATAAATAATATAA
1 ATATTAATAAATAATATAA
13875 AGAATAATAA
Statistics
Matches: 91, Mismatches: 8, Indels: 10
0.83 0.07 0.09
Matches are distributed among these distances:
40 7 0.08
41 44 0.48
42 2 0.02
43 2 0.02
44 29 0.32
45 7 0.08
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (41 bp):
ATATTAATAAATAATATAATATTAATAAATAATATTATAAT
Found at i:13795 original size:59 final size:62
Alignment explanation
Indices: 13731--13849 Score: 183
Period size: 59 Copynumber: 2.0 Consensus size: 62
13721 TTTTTTACAA
13731 TATTAACAAATAATATAATATTAATA-AATAATATT-AT-AATA-TATTAATAAATAATATAT
1 TATTAACAAATAATATAATATTAATATAAT-ATATTAATAAATATTATTAATAAATAATATAT
* *
13790 TATTAATAAATAATATACTATTAATATAATATATTAATAAATATTATTAATAAATAATAT
1 TATTAACAAATAATATAATATTAATATAATATATTAATAAATATTATTAATAAATAATAT
13850 TATACTATAT
Statistics
Matches: 54, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
59 29 0.54
60 5 0.09
61 4 0.07
62 16 0.30
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (62 bp):
TATTAACAAATAATATAATATTAATATAATATATTAATAAATATTATTAATAAATAATATAT
Found at i:13859 original size:26 final size:24
Alignment explanation
Indices: 13739--13872 Score: 102
Period size: 26 Copynumber: 5.5 Consensus size: 24
13729 AATATTAACA
13739 AATAATATAATATTAATAAATAATATT
1 AATAA-ATAATATTAAT-AAT-ATATT
* *
13766 -ATAATATATTAATAAATAATATATT
1 AATAA-ATAAT-ATTAATAATATATT
*
13791 -ATTAATAA-A-TAAT-ATACTATT
1 AATAAATAATATTAATAATA-TATT
13812 AATATAAT-ATATTAATAAATATTATT
1 AATA-AATAATATTAAT-AATA-TATT
*
13838 AATAAATAATATT-ATACTATATT
1 AATAAATAATATTAATAATATATT
13861 AATAAATAATAT
1 AATAAATAATAT
13873 AAAGAATAAT
Statistics
Matches: 90, Mismatches: 8, Indels: 22
0.75 0.07 0.18
Matches are distributed among these distances:
20 3 0.03
21 7 0.08
22 4 0.04
23 20 0.22
24 10 0.11
25 13 0.14
26 28 0.31
27 5 0.06
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (24 bp):
AATAAATAATATTAATAATATATT
Found at i:13872 original size:23 final size:22
Alignment explanation
Indices: 13781--13868 Score: 72
Period size: 23 Copynumber: 3.8 Consensus size: 22
13771 ATATTAATAA
* * *
13781 ATAATATATT-ATTAATAAATA
1 ATAATATATTAATAAATATATT
13802 AT-ATACTATTAATATAATATATT
1 ATAATA-TATTAATA-AATATATT
13825 AATAAATATTATTAATAAATAATATT
1 -AT-AATA-TATTAATAAAT-ATATT
*
13851 ATACTATATTAATAAATA
1 ATAATATATTAATAAATA
13869 ATATAAAGAA
Statistics
Matches: 55, Mismatches: 5, Indels: 13
0.75 0.07 0.18
Matches are distributed among these distances:
20 3 0.05
21 6 0.11
22 3 0.05
23 17 0.31
24 5 0.09
25 5 0.09
26 16 0.29
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (22 bp):
ATAATATATTAATAAATATATT
Found at i:13941 original size:18 final size:18
Alignment explanation
Indices: 13901--13967 Score: 57
Period size: 19 Copynumber: 3.8 Consensus size: 18
13891 TTATTTTAAG
* *
13901 TATTTTTATATTAACATAA
1 TATTTTAATATTAA-ATAT
13920 TATTTTAATATTAAATAT
1 TATTTTAATATTAAATAT
** * *
13938 TATTAAAATA-TAATTGT
1 TATTTTAATATTAAATAT
13955 T-TTTTAATATTAA
1 TATTTTAATATTAA
13968 TAATTTTTAT
Statistics
Matches: 39, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
16 6 0.15
17 9 0.23
18 11 0.28
19 13 0.33
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54
Consensus pattern (18 bp):
TATTTTAATATTAAATAT
Found at i:14006 original size:26 final size:25
Alignment explanation
Indices: 13966--14029 Score: 85
Period size: 26 Copynumber: 2.5 Consensus size: 25
13956 TTTTAATATT
*
13966 AATAATTTTTATAATAAATAATTTC
1 AATAATTTTAATAATAAATAATTTC
*
13991 AATACATTTTAATAATAAATAATTTTT
1 AATA-ATTTTAATAATAAATAA-TTTC
14018 AAT-ATTTTAATA
1 AATAATTTTAATA
14030 GTTATATTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
25 13 0.37
26 16 0.46
27 6 0.17
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (25 bp):
AATAATTTTAATAATAAATAATTTC
Found at i:14024 original size:25 final size:25
Alignment explanation
Indices: 13959--14029 Score: 90
Period size: 25 Copynumber: 2.8 Consensus size: 25
13949 AATTGTTTTT
* *
13959 TAATATTAATAATTTTTATAATAAA
1 TAATTTTAATAATTTTAATAATAAA
*
13984 TAATTTCAATACATTTTAATAATAAA
1 TAATTTTAATA-ATTTTAATAATAAA
14010 TAATTTTTAAT-ATTTTAATA
1 TAA-TTTTAATAATTTTAATA
14030 GTTATATTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
25 18 0.45
26 16 0.40
27 6 0.15
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.49
Consensus pattern (25 bp):
TAATTTTAATAATTTTAATAATAAA
Found at i:14168 original size:13 final size:14
Alignment explanation
Indices: 14152--14181 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
14142 ATATAAATAT
14152 TTTTC-AAAAATTA
1 TTTTCAAAAAATTA
14165 TTTTCAAAAAATTA
1 TTTTCAAAAAATTA
14179 TTT
1 TTT
14182 ATTGCGAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.31
14 11 0.69
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.50
Consensus pattern (14 bp):
TTTTCAAAAAATTA
Found at i:16517 original size:9 final size:9
Alignment explanation
Indices: 16500--16534 Score: 61
Period size: 9 Copynumber: 3.9 Consensus size: 9
16490 TTACATTAAT
16500 AATAATAAC
1 AATAATAAC
*
16509 AACAATAAC
1 AATAATAAC
16518 AATAATAAC
1 AATAATAAC
16527 AATAATAA
1 AATAATAA
16535 TAAACATGTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.69, C:0.11, G:0.00, T:0.20
Consensus pattern (9 bp):
AATAATAAC
Found at i:17166 original size:15 final size:16
Alignment explanation
Indices: 17141--17205 Score: 75
Period size: 16 Copynumber: 4.2 Consensus size: 16
17131 AAGAAATATT
17141 AAAATATATATAATAA
1 AAAATATATATAATAA
*
17157 AAAATA-ATATAA-AT
1 AAAATATATATAATAA
*
17171 AAAA-AT-GATAATAA
1 AAAATATATATAATAA
17185 ATAAATATATATAATAA
1 A-AAATATATATAATAA
17202 AAAA
1 AAAA
17206 GCTTGGCCTA
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
13 5 0.12
14 7 0.17
15 9 0.22
16 11 0.28
17 8 0.20
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.28
Consensus pattern (16 bp):
AAAATATATATAATAA
Found at i:17194 original size:28 final size:29
Alignment explanation
Indices: 17150--17204 Score: 87
Period size: 28 Copynumber: 1.9 Consensus size: 29
17140 TAAAATATAT
17150 ATAATAAAAAATAATATA-AATAAAAATG
1 ATAATAAAAAATAATATATAATAAAAATG
17178 ATAATAAATAAAT-ATATATAATAAAAA
1 ATAATAAA-AAATAATATATAATAAAAA
17205 AGCTTGGCCT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
28 13 0.52
29 12 0.48
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (29 bp):
ATAATAAAAAATAATATATAATAAAAATG
Found at i:18798 original size:3 final size:3
Alignment explanation
Indices: 18790--18833 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
18780 AACTCAAAAT
18790 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
18834 TTCACCTAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:18889 original size:16 final size:15
Alignment explanation
Indices: 18858--18892 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
18848 AAAGAATTAT
*
18858 TAAATAATAAAATAA
1 TAAAGAATAAAATAA
18873 TAAAGAATAAGAATAA
1 TAAAGAATAA-AATAA
18889 TAAA
1 TAAA
18893 ATTTTAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.71, C:0.00, G:0.06, T:0.23
Consensus pattern (15 bp):
TAAAGAATAAAATAA
Found at i:24162 original size:31 final size:32
Alignment explanation
Indices: 24111--24171 Score: 79
Period size: 31 Copynumber: 1.9 Consensus size: 32
24101 CCCATATTAG
* **
24111 TTGGCATCAATGAAGTTTTAAACC-AGTTTCA
1 TTGGCATCAATCAAAATTTAAACCTAGTTTCA
*
24142 TTGGCATCAATCAAAATTTAAGCCTAGTTT
1 TTGGCATCAATCAAAATTTAAACCTAGTTT
24172 AGTTGGTATG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
31 20 0.80
32 5 0.20
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.36
Consensus pattern (32 bp):
TTGGCATCAATCAAAATTTAAACCTAGTTTCA
Found at i:24261 original size:32 final size:32
Alignment explanation
Indices: 24193--24261 Score: 77
Period size: 32 Copynumber: 2.2 Consensus size: 32
24183 AAGCCAATAT
* * * *
24193 TAGCTAGCACCAATGAAGTTGTAAGGTTAGTT
1 TAGCTAGCACCAATGAAATTGTAAGCTCAGTC
*
24225 TAGCTAGCATCAATCGAAATT-TAAGCTCAGTC
1 TAGCTAGCACCAAT-GAAATTGTAAGCTCAGTC
24257 TAGCT
1 TAGCT
24262 GACATATAAG
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
32 26 0.84
33 5 0.16
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.30
Consensus pattern (32 bp):
TAGCTAGCACCAATGAAATTGTAAGCTCAGTC
Found at i:24621 original size:32 final size:32
Alignment explanation
Indices: 24536--24839 Score: 155
Period size: 32 Copynumber: 9.2 Consensus size: 32
24526 AAAATAAAAT
* * *
24536 TTTAAGCTCAGATTA-CTTGGTACTCAATGAAA
1 TTTAAGCCCAGATTATC-TGGCACCCAATGAAA
*
24568 GTTTAAGCCTAGATTATCTGGCACCCAATGAAA
1 -TTTAAGCCCAGATTATCTGGCACCCAATGAAA
* * *
24601 TTTAAGCCCA-ATTTAACTGGCACTCGATGAAAAAA
1 TTTAAGCCCAGA-TTATCTGGCACCCAATG---AAA
* * * *
24636 TTTAAACCCAGATTACCTAGCACTCAATGAAA
1 TTTAAGCCCAGATTATCTGGCACCCAATGAAA
* * * *
24668 TTTTAAGTCTAAATTATCTGGCACCAAATGAAA
1 -TTTAAGCCCAGATTATCTGGCACCCAATGAAA
***** ** *
24701 TTTAAAATTGGATTATCTGGCTTCTAATGAAA
1 TTTAAGCCCAGATTATCTGGCACCCAATGAAA
* * * * *
24733 TTTAAGCCTAGTTTAGCTAGCACTCAATGAAAAA
1 TTTAAGCCCAGATTATCTGGCACCCAATG--AAA
* * * *
24767 TTTAAAG-CCATATTACCTCGCACTCAATGAAA
1 TTT-AAGCCCAGATTATCTGGCACCCAATGAAA
* * * * *
24799 TTTTAGGCCTAAATTATCTAGCGCCCAATGAAA
1 -TTTAAGCCCAGATTATCTGGCACCCAATGAAA
24832 TTTAAGCC
1 TTTAAGCC
24840 TGATTTAGTT
Statistics
Matches: 207, Mismatches: 52, Indels: 25
0.73 0.18 0.09
Matches are distributed among these distances:
31 1 0.00
32 80 0.39
33 72 0.35
34 24 0.12
35 29 0.14
36 1 0.00
ACGTcount: A:0.37, C:0.19, G:0.14, T:0.31
Consensus pattern (32 bp):
TTTAAGCCCAGATTATCTGGCACCCAATGAAA
Found at i:24659 original size:35 final size:35
Alignment explanation
Indices: 24598--24667 Score: 88
Period size: 35 Copynumber: 2.0 Consensus size: 35
24588 GCACCCAATG
* * *
24598 AAATTTAAGCCCAATTTAACTGGCACTCGATGAAA
1 AAATTTAAACCCAATTTAACTAGCACTCAATGAAA
*
24633 AAATTTAAACCCAGA-TTACCTAGCACTCAATGAAA
1 AAATTTAAACCCA-ATTTAACTAGCACTCAATGAAA
24668 TTTTAAGTCT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
35 29 0.97
36 1 0.03
ACGTcount: A:0.43, C:0.21, G:0.11, T:0.24
Consensus pattern (35 bp):
AAATTTAAACCCAATTTAACTAGCACTCAATGAAA
Found at i:24770 original size:34 final size:32
Alignment explanation
Indices: 24726--24846 Score: 95
Period size: 34 Copynumber: 3.7 Consensus size: 32
24716 TCTGGCTTCT
*
24726 AATG-AAATTTAAGCCTAGTTTAGCTAGCACTC
1 AATGAAAATTTAAGCCTA-TTTACCTAGCACTC
*
24758 AATGAAAAATTTAAAGCC-ATATTACCTCGCACTC
1 AATG-AAAATTT-AAGCCTAT-TTACCTAGCACTC
* * * * * *
24792 AATGAAATTTTAGGCCTAAATTATCTAGCGCCC
1 AATGAAAATTTAAGCCT-ATTTACCTAGCACTC
24825 AATG-AAATTTAAGCCTGATTTA
1 AATGAAAATTTAAGCCT-ATTTA
24847 GTTAGCTCTT
Statistics
Matches: 70, Mismatches: 13, Indels: 12
0.74 0.14 0.13
Matches are distributed among these distances:
32 22 0.31
33 20 0.29
34 23 0.33
35 5 0.07
ACGTcount: A:0.37, C:0.19, G:0.13, T:0.31
Consensus pattern (32 bp):
AATGAAAATTTAAGCCTATTTACCTAGCACTC
Found at i:24815 original size:131 final size:132
Alignment explanation
Indices: 24579--24836 Score: 365
Period size: 131 Copynumber: 2.0 Consensus size: 132
24569 TTTAAGCCTA
* *
24579 GATTATCTGGCACCCAATGAAATTTAAGCCCAATTTAACTGGCACTCGATGAAAAAATTTAAACC
1 GATTATCTGGCACCCAATGAAATTTAAGCCCAATTTAACTAGCACTCAATGAAAAAATTTAAACC
* *
24644 CAGATTACCTAGCACTCAATGAAATTTTAAGTCTAAATTATCTGGCACCAAATGAAATTTAAAAT
66 CAGATTACCTAGCACTCAATGAAATTTTAAGCCTAAATTATCTAGCACCAAATGAAATTTAAAAT
24709 TG
131 TG
** * * * * *
24711 GATTATCTGGCTTCTAATGAAATTTAAGCCTAGTTTAGCTAGCACTCAATG-AAAAATTTAAAGC
1 GATTATCTGGCACCCAATGAAATTTAAGCCCAATTTAACTAGCACTCAATGAAAAAATTTAAACC
* * * * *
24775 CATATTACCTCGCACTCAATGAAATTTTAGGCCTAAATTATCTAGCGCCCAATGAAATTTAA
66 CAGATTACCTAGCACTCAATGAAATTTTAAGCCTAAATTATCTAGCACCAAATGAAATTTAA
24837 GCCTGATTTA
Statistics
Matches: 110, Mismatches: 16, Indels: 1
0.87 0.13 0.01
Matches are distributed among these distances:
131 67 0.61
132 43 0.39
ACGTcount: A:0.38, C:0.19, G:0.13, T:0.30
Consensus pattern (132 bp):
GATTATCTGGCACCCAATGAAATTTAAGCCCAATTTAACTAGCACTCAATGAAAAAATTTAAACC
CAGATTACCTAGCACTCAATGAAATTTTAAGCCTAAATTATCTAGCACCAAATGAAATTTAAAAT
TG
Found at i:24977 original size:32 final size:31
Alignment explanation
Indices: 24936--25012 Score: 84
Period size: 31 Copynumber: 2.4 Consensus size: 31
24926 AGTTGGCACT
*
24936 CAATGAAAATTTAAGCTCAACT-TAGCTGATATC
1 CAAT-AAAATTTAAG-TCAACTGTAGCTGACA-C
* * *
24969 CAATAAAATTTAAGTCTAGTGTAGTTGACAC
1 CAATAAAATTTAAGTCAACTGTAGCTGACAC
25000 CAATAAAATTTAA
1 CAATAAAATTTAA
25013 ACCTAGTTTA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
31 18 0.46
32 17 0.44
33 4 0.10
ACGTcount: A:0.43, C:0.14, G:0.12, T:0.31
Consensus pattern (31 bp):
CAATAAAATTTAAGTCAACTGTAGCTGACAC
Found at i:25242 original size:14 final size:14
Alignment explanation
Indices: 25201--25246 Score: 58
Period size: 14 Copynumber: 3.3 Consensus size: 14
25191 CATCTTAAGA
*
25201 AAAAAATAAAAAAC
1 AAAAAATAAAAACC
25215 AAAAAA-AAATAACC
1 AAAAAATAAA-AACC
*
25229 AAAAAATAACAACC
1 AAAAAATAAAAACC
25243 AAAA
1 AAAA
25247 CCAAAAAAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
13 3 0.11
14 23 0.82
15 2 0.07
ACGTcount: A:0.80, C:0.13, G:0.00, T:0.07
Consensus pattern (14 bp):
AAAAAATAAAAACC
Found at i:25621 original size:15 final size:14
Alignment explanation
Indices: 25601--25646 Score: 58
Period size: 15 Copynumber: 3.2 Consensus size: 14
25591 CGTTACATAT
25601 ATAAAAATAATAATA
1 ATAAAAATAA-AATA
25616 ATAAAAAGTAAAATA
1 ATAAAAA-TAAAATA
*
25631 TTAAAAATAAAA-A
1 ATAAAAATAAAATA
25644 ATA
1 ATA
25647 CGTATGTAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
13 3 0.11
14 5 0.18
15 17 0.61
16 3 0.11
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.24
Consensus pattern (14 bp):
ATAAAAATAAAATA
Found at i:25629 original size:21 final size:21
Alignment explanation
Indices: 25604--25643 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
25594 TACATATATA
*
25604 AAAATAATAATAATAAAAAGT
1 AAAATAATAAAAATAAAAAGT
*
25625 AAAATATTAAAAATAAAAA
1 AAAATAATAAAAATAAAAA
25644 ATACGTATGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.75, C:0.00, G:0.03, T:0.23
Consensus pattern (21 bp):
AAAATAATAAAAATAAAAAGT
Found at i:25715 original size:16 final size:16
Alignment explanation
Indices: 25690--25737 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
25680 AAATTAAAAC
25690 ATATATAATAAAAAATA
1 ATATA-AATAAAAAATA
*
25707 ATATAAATAAAAATTA
1 ATATAAATAAAAAATA
*
25723 ATATATATAATAAAA
1 ATATAAATAA-AAAA
25738 AAGTTTAACC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
16 19 0.70
17 8 0.30
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (16 bp):
ATATAAATAAAAAATA
Found at i:27751 original size:7 final size:7
Alignment explanation
Indices: 27741--27765 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
27731 ATTTTTTAAA
27741 AAATAAT
1 AAATAAT
27748 AAATAAT
1 AAATAAT
27755 AAATAAT
1 AAATAAT
27762 AAAT
1 AAAT
27766 TAAGATTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (7 bp):
AAATAAT
Found at i:30407 original size:26 final size:27
Alignment explanation
Indices: 30352--30407 Score: 62
Period size: 28 Copynumber: 2.1 Consensus size: 27
30342 ATATTTAAGA
* *
30352 AATTTTATTTCATTAAAAATTTTCATAT
1 AATTTTATTT-ATTAAAAATATTCAAAT
30380 AATTTTATTT-TTAAAAAATATT-AAAT
1 AATTTTATTTATT-AAAAATATTCAAAT
30406 AA
1 AA
30408 AGAATAATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
26 7 0.28
27 8 0.32
28 10 0.40
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (27 bp):
AATTTTATTTATTAAAAATATTCAAAT
Found at i:32468 original size:21 final size:21
Alignment explanation
Indices: 32442--32488 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
32432 TGAAAAAAAT
32442 AAAAATTTCAAAACTTT-TTTA
1 AAAAATTT-AAAACTTTATTTA
*
32463 AAAAA-TTAAAATTTTATTTA
1 AAAAATTTAAAACTTTATTTA
32483 AAAAAT
1 AAAAAT
32489 AAACTAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
19 7 0.30
20 11 0.48
21 5 0.22
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.40
Consensus pattern (21 bp):
AAAAATTTAAAACTTTATTTA
Done.