Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015171.1 Corchorus olitorius cultivar O-4 contig15204, 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: 53236
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:6351 original size:13 final size:13
Alignment explanation
Indices: 6333--6361 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
6323 CCCCTGGGGT
6333 TTTTTTTATTTTA
1 TTTTTTTATTTTA
6346 TTTTTTTATTTTA
1 TTTTTTTATTTTA
6359 TTT
1 TTT
6362 CGTTTATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (13 bp):
TTTTTTTATTTTA
Found at i:8024 original size:19 final size:19
Alignment explanation
Indices: 8000--8036 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
7990 CTGTTTAGCA
8000 ACTGTACAGATGAGATTAC
1 ACTGTACAGATGAGATTAC
* *
8019 ACTGTACATATTAGATTA
1 ACTGTACAGATGAGATTA
8037 GGTACTGTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.32
Consensus pattern (19 bp):
ACTGTACAGATGAGATTAC
Found at i:9199 original size:17 final size:15
Alignment explanation
Indices: 9177--9222 Score: 56
Period size: 15 Copynumber: 2.9 Consensus size: 15
9167 ATGCGATTAC
9177 AATATTTATATATATAT
1 AATATTTATA-ATA-AT
9194 AATATTTATAATAAT
1 AATATTTATAATAAT
* *
9209 AATAATAATAATAA
1 AATATTTATAATAA
9223 AAAAGATGGT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
15 14 0.52
16 3 0.11
17 10 0.37
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
AATATTTATAATAAT
Found at i:16663 original size:31 final size:29
Alignment explanation
Indices: 16628--16723 Score: 70
Period size: 31 Copynumber: 3.2 Consensus size: 29
16618 ATTGCTCGAG
16628 TAAGGGCCTAACATTTGTCAAAATGCTCAAA
1 TAAGGGCCTAAC-TTT-TCAAAATGCTCAAA
* * **
16659 TAAGGGTCCGATCTTTT-AATTTAGCT-AAA
1 TAAGGG-CCTAACTTTTCAAAAT-GCTCAAA
* *
16688 TAAGGGCCTAACGTTTACCAAAATACTCAAA
1 TAAGGGCCTAAC-TTT-TCAAAATGCTCAAA
16719 TAAGG
1 TAAGG
16724 ACTCGGTCGT
Statistics
Matches: 49, Mismatches: 10, Indels: 12
0.69 0.14 0.17
Matches are distributed among these distances:
28 4 0.08
29 15 0.31
30 6 0.12
31 20 0.41
32 4 0.08
ACGTcount: A:0.38, C:0.18, G:0.17, T:0.28
Consensus pattern (29 bp):
TAAGGGCCTAACTTTTCAAAATGCTCAAA
Found at i:16696 original size:60 final size:59
Alignment explanation
Indices: 16628--16787 Score: 187
Period size: 60 Copynumber: 2.7 Consensus size: 59
16618 ATTGCTCGAG
* * *
16628 TAAGGGCCTAACATTTGTCAAAATGCTCAAATAAGGGTCCGATCTTTTAATTTAGCTAAA
1 TAAGGGCCTAAC-TTTATCAAAATGCTCAAATAAGGGTCCGATCGTTTAATTTAGCCAAA
* * * * *
16688 TAAGGGCCTAACGTTTACCAAAATACTCAAATAA-GGACTCGGTCGTTTAATTTGGCCAAA
1 TAAGGGCCTAAC-TTTATCAAAATGCTCAAATAAGGGTC-CGATCGTTTAATTTAGCCAAA
* *
16748 TAAGGGCCTAACGTTATCGAAAATGTTCAAATAAGGGTCC
1 TAAGGGCCTAACTTTATC-AAAATGCTCAAATAAGGGTCC
16788 AGCGTCAGTT
Statistics
Matches: 83, Mismatches: 14, Indels: 6
0.81 0.14 0.06
Matches are distributed among these distances:
59 7 0.08
60 73 0.88
61 3 0.04
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.28
Consensus pattern (59 bp):
TAAGGGCCTAACTTTATCAAAATGCTCAAATAAGGGTCCGATCGTTTAATTTAGCCAAA
Found at i:16926 original size:60 final size:60
Alignment explanation
Indices: 16830--16945 Score: 160
Period size: 60 Copynumber: 1.9 Consensus size: 60
16820 GACGCCAGAT
* * * *
16830 CCTTATTTGAGCATTTTCGATAACATTATGCTCTTATTTGGCCAAATTATAAGATCAGTC
1 CCTTATTTCAGCATTTTCGATAACATTATACCCTTATTTGGCCAAATTAAAAGATCAGTC
* ** *
16890 CCTTATTTCAGCATTTTTGATAATTTTATACCCTTATTTGGCTAAATTAAAAGATC
1 CCTTATTTCAGCATTTTCGATAACATTATACCCTTATTTGGCCAAATTAAAAGATC
16946 GAGCCCTATT
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
60 48 1.00
ACGTcount: A:0.29, C:0.17, G:0.11, T:0.42
Consensus pattern (60 bp):
CCTTATTTCAGCATTTTCGATAACATTATACCCTTATTTGGCCAAATTAAAAGATCAGTC
Found at i:18718 original size:9 final size:9
Alignment explanation
Indices: 18700--18739 Score: 53
Period size: 9 Copynumber: 4.4 Consensus size: 9
18690 GGACAGTTAT
18700 GAAGATGAG
1 GAAGATGAG
*
18709 GAAGAGGAG
1 GAAGATGAG
18718 GAAGATGAG
1 GAAGATGAG
* *
18727 GAAAACGAG
1 GAAGATGAG
18736 GAAG
1 GAAG
18740 TGGAAGGTAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.47, C:0.03, G:0.45, T:0.05
Consensus pattern (9 bp):
GAAGATGAG
Found at i:18723 original size:18 final size:18
Alignment explanation
Indices: 18700--18739 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
18690 GGACAGTTAT
* *
18700 GAAGATGAGGAAGAGGAG
1 GAAGATGAGGAAAACGAG
18718 GAAGATGAGGAAAACGAG
1 GAAGATGAGGAAAACGAG
18736 GAAG
1 GAAG
18740 TGGAAGGTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.47, C:0.03, G:0.45, T:0.05
Consensus pattern (18 bp):
GAAGATGAGGAAAACGAG
Found at i:37524 original size:203 final size:202
Alignment explanation
Indices: 37166--37542 Score: 605
Period size: 203 Copynumber: 1.9 Consensus size: 202
37156 ATATATGTTG
* ** * * *
37166 GTGGAGTTTAGCAGATTGTACATGCGGGTCTTGAAGGGTGATATGTGTCCTCTAAGGACTAGATT
1 GTGGAGTTTAGCAGACTACACATGCGGGTCCTGAAAGGTGACATGTGTCCTCTAAGGACTAGATT
* *
37231 GAAATATTTAAAATTTAATTAATTCAGAAAATAGACATGTGTCAACTCCACAACCTGCTTGTGAA
66 GAAATATTTAAAATTTAATTAATTCAAAAAATAGACATGTGTCAACTCCACAACCCGCTTGTGAA
*
37296 GTCCAAATTTTACACCGTCGGTGTATCAAATAATTACCCATTAATAAAACGCTAAATATACAATA
131 GTCCAAAATTTACACCGTCGGTGTATCAAATAATTACCC-TTAATAAAACGCTAAATATACAATA
37361 CAACGTCA
195 CAACGTCA
*
37369 GTGGAGTTTAGCAGACTACACATGCGGGTCCTGAAAGGTGACATGTGTCCTCTAGGGACTAGATT
1 GTGGAGTTTAGCAGACTACACATGCGGGTCCTGAAAGGTGACATGTGTCCTCTAAGGACTAGATT
*
37434 GAAATATTTAAAATTTAATTAATT-AAAACAATGGACATGTGTCAACTCCACAACCCGCTTGTGA
66 GAAATATTTAAAATTTAATTAATTCAAAA-AATAGACATGTGTCAACTCCACAACCCGCTTGTGA
*
37498 AGTCCAAAATTTACACTGAT-GGTGTATCAAATAATTACCCTTAAT
130 AGTCCAAAATTTACACCG-TCGGTGTATCAAATAATTACCCTTAAT
37543 TAAATGTTTA
Statistics
Matches: 160, Mismatches: 12, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
202 8 0.05
203 151 0.94
204 1 0.01
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.30
Consensus pattern (202 bp):
GTGGAGTTTAGCAGACTACACATGCGGGTCCTGAAAGGTGACATGTGTCCTCTAAGGACTAGATT
GAAATATTTAAAATTTAATTAATTCAAAAAATAGACATGTGTCAACTCCACAACCCGCTTGTGAA
GTCCAAAATTTACACCGTCGGTGTATCAAATAATTACCCTTAATAAAACGCTAAATATACAATAC
AACGTCA
Found at i:42509 original size:30 final size:30
Alignment explanation
Indices: 42473--42534 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 30
42463 GTTAATAAGC
* *
42473 CATTAAAATTTGAGGGTATAAGAGAAAAGT
1 CATTAAAATTCGAGGGTATAAAAGAAAAGT
*
42503 CATTAAAATTCGAGGGTATAAAAGGAAAGT
1 CATTAAAATTCGAGGGTATAAAAGAAAAGT
42533 CA
1 CA
42535 AGATAAAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.47, C:0.06, G:0.23, T:0.24
Consensus pattern (30 bp):
CATTAAAATTCGAGGGTATAAAAGAAAAGT
Found at i:45273 original size:14 final size:14
Alignment explanation
Indices: 45254--45281 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
45244 ACTATGCGGT
45254 TGGATTTCAATGTA
1 TGGATTTCAATGTA
45268 TGGATTTCAATGTA
1 TGGATTTCAATGTA
45282 CTATTTATAT
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:0.29, C:0.07, G:0.21, T:0.43
Consensus pattern (14 bp):
TGGATTTCAATGTA
Found at i:46655 original size:14 final size:15
Alignment explanation
Indices: 46626--46665 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
46616 AATTTAGAAA
46626 TATATCTATATCTATC
1 TATAT-TATATCTATC
*
46642 TATA-TATATTTATC
1 TATATTATATCTATC
46656 TATATTATAT
1 TATATTATAT
46666 ATAAAAGTAC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
14 13 0.59
15 5 0.23
16 4 0.18
ACGTcount: A:0.35, C:0.10, G:0.00, T:0.55
Consensus pattern (15 bp):
TATATTATATCTATC
Found at i:47135 original size:22 final size:22
Alignment explanation
Indices: 46973--47273 Score: 193
Period size: 22 Copynumber: 13.8 Consensus size: 22
46963 AATTTTGGAA
* * *
46973 GTTATCAAAA-TTCATTGTGTG
1 GTTATCAAAATTTCATAGGGAG
* * *
46994 GTTA-CTAAAATTTTATAGTGCG
1 GTTATC-AAAATTTCATAGGGAG
* * * *
47016 GTTCTCAAAATTTTATAGTGTG
1 GTTATCAAAATTTCATAGGGAG
* * *
47038 GTTACCAAAATTTCATAGGTAA
1 GTTATCAAAATTTCATAGGGAG
* * * * *
47060 GATGTTAAAATTTTATAGTGTA-
1 GTTATCAAAATTTCATAG-GGAG
* *
47082 GTTATCACAATTTCAT-GGGAT
1 GTTATCAAAATTTCATAGGGAG
*
47103 GTTATCAAAATTTCATAAGGAG
1 GTTATCAAAATTTCATAGGGAG
* *
47125 ATTATCGAAA-TTCAT-GGGAAG
1 GTTATCAAAATTTCATAGGG-AG
*
47146 GTTGTCAAAATTTCATAGGGAG
1 GTTATCAAAATTTCATAGGGAG
* ****
47168 GTTACCAAAATTTCATATTCTG
1 GTTATCAAAATTTCATAGGGAG
*
47190 GTTATCAAAATTTCATAGGGCG
1 GTTATCAAAATTTCATAGGGAG
* * *
47212 ATTATCGAAATCTT-ATATGGAG
1 GTTATCAAAAT-TTCATAGGGAG
* *
47234 GTTATTAAAATTTCATAGGAAG
1 GTTATCAAAATTTCATAGGGAG
*
47256 ATTATCAAAATTTCATAG
1 GTTATCAAAATTTCATAG
47274 TATGCTTATA
Statistics
Matches: 215, Mismatches: 54, Indels: 21
0.74 0.19 0.07
Matches are distributed among these distances:
20 5 0.02
21 40 0.19
22 161 0.75
23 9 0.04
ACGTcount: A:0.35, C:0.10, G:0.18, T:0.37
Consensus pattern (22 bp):
GTTATCAAAATTTCATAGGGAG
Found at i:47288 original size:44 final size:44
Alignment explanation
Indices: 47066--47928 Score: 220
Period size: 44 Copynumber: 19.8 Consensus size: 44
47056 GTAAGATGTT
* * * *
47066 AAAATTTTATAGTGTAG-TTATCACAATTTCATGGGAT-GTTATC
1 AAAATTTCATAG-GGAGATTATCAAAATTTCATAGGATGGTTATC
* * * * *
47109 AAAATTTCATAAGGAGATTATCGAAA-TTCATGGGAAGGTTGTC
1 AAAATTTCATAGGGAGATTATCAAAATTTCATAGGATGGTTATC
* * ***
47152 AAAATTTCATAGGGAGGTTACCAAAATTTCATATTCTGGTTATC
1 AAAATTTCATAGGGAGATTATCAAAATTTCATAGGATGGTTATC
* * *
47196 AAAATTTCATAGGGCGATTATCGAAATCTT-ATATGGA-GGTTATT
1 AAAATTTCATAGGGAGATTATCAAAAT-TTCATA-GGATGGTTATC
* * * *
47240 AAAATTTCATAGGAAGATTATCAAAATTTCATAGTATGCTTATAA
1 AAAATTTCATAGGGAGATTATCAAAATTTCATAGGATGGTTAT-C
* * * *
47285 AAATTACTTAGTGAGATAGAGTGAGCTTATCAAAATTTCA-AGTG-TTGTTACC
1 AAA--A-TT--T--CATAG-G-GAGATTATCAAAATTTCATAG-GATGGTTATC
* * * * *
47337 AAAATTTCATA-GTATAATAGTCACAATTTCATA-GA-GG-TAAC
1 AAAATTTCATAGGGAGATTA-TCAAAATTTCATAGGATGGTTATC
* * * ** * * *
47378 AAAATTTGATGGGGAGGTTATTGAAATTTTAGAGGGGA-GATTATC
1 AAAATTTCATAGGGAGATTATCAAAATTTCATA--GGATGGTTATC
* * * * **
47423 AAAATTTCATAGTGTGGTTATCAAAATTTTATA--AT-GTGGT-
1 AAAATTTCATAGGGAGATTATCAAAATTTCATAGGATGGTTATC
* * * ** *
47463 ---ATTTCAGAGGGAGAGATTATCAAATTTTCATTGTTTGG-TAGTT
1 AAAATTTCATA-GG-GAGATTATCAAAATTTCATAGGATGGTTA-TC
** * *
47506 AAAATTTCATAATGAGTTTATCAAAATTT-ATA--ATGAGATTAAC
1 AAAATTTCATAGGGAGATTATCAAAATTTCATAGGATG-G-TTATC
* * * * * * * **
47549 AAAATTTGATAGTGTGGTTCTCAAAATTTTATAGGGA-GATTAAGA
1 AAAATTTCATAGGGAGATTATCAAAATTTCATA-GGATGGTT-ATC
* ** * **
47594 AAAATTTCATAGGTA-AGTTATCGTAATTTTAT-GCTGTAATTAATTATC
1 AAAATTTCATAGGGAGA-TTATCAAAATTTCATAG--G--A-TGGTTATC
* * * **
47642 AAAATTTCATTGGG-GGTTATCAAAATTTAATAGTG-TTTTTATC
1 AAAATTTCATAGGGAGATTATCAAAATTTCATAG-GATGGTTATC
* * * *
47685 AAAATTTCGTA-GGAGGTTAACAAAAGTTT-AT--GA-GGTTATAA
1 AAAATTTCATAGGGAGATTATCAAAA-TTTCATAGGATGGTTAT-C
*
47726 AAAATTT-ATAGGGATG-TTATCAAAATTTCATAAGATGGTTATC
1 AAAATTTCATAGGGA-GATTATCAAAATTTCATAGGATGGTTATC
*
47769 AAAATTTCATGAGGTG-G-TTTTCAAAATTTCAT--GA-GGTTATC
1 AAAATTTCAT-AGG-GAGATTATCAAAATTTCATAGGATGGTTATC
* * *
47810 AAAATTTCAT---GAGGTTATCAAAATTTGAAATGGA-GGTTATC
1 AAAATTTCATAGGGAGATTATCAAAATTTCATA-GGATGGTTATC
* *
47851 AAAATGTT-ATAGGGAGGTTTATAAAAAATTTCATAGTGA-GG-TATC
1 AAAAT-TTCATAGGGA-GATTAT-CAAAATTTCATAG-GATGGTTATC
* * *
47896 ACAATTTCAT-GGTATGTTTATCAAAATTTCATA
1 AAAATTTCATAGGGA-GATTATCAAAATTTCATA
47929 ATGTGATTAC
Statistics
Matches: 603, Mismatches: 137, Indels: 160
0.67 0.15 0.18
Matches are distributed among these distances:
36 1 0.00
37 8 0.01
38 13 0.02
39 15 0.02
40 10 0.02
41 79 0.13
42 31 0.05
43 133 0.22
44 139 0.23
45 81 0.13
46 22 0.04
47 18 0.03
48 16 0.03
49 5 0.01
50 2 0.00
52 7 0.01
53 7 0.01
54 16 0.03
ACGTcount: A:0.37, C:0.08, G:0.18, T:0.37
Consensus pattern (44 bp):
AAAATTTCATAGGGAGATTATCAAAATTTCATAGGATGGTTATC
Found at i:47445 original size:22 final size:22
Alignment explanation
Indices: 47418--48057 Score: 160
Period size: 22 Copynumber: 29.5 Consensus size: 22
47408 AGAGGGGAGA
47418 TTATCAAAATTTCATAGTGTGG
1 TTATCAAAATTTCATAGTGTGG
* *
47440 TTATCAAAATTTTATAATGTGG
1 TTATCAAAATTTCATAGTGTGG
* * *
47462 ---T----ATTTCAGAGGGAGAG
1 TTATCAAAATTTCATAGTGTG-G
* * *
47478 ATTATCAAATTTTCATTGTTTGG
1 -TTATCAAAATTTCATAGTGTGG
* * * *
47501 -TAGTTAAAATTTCATAATGAGT
1 TTA-TCAAAATTTCATAGTGTGG
* * *
47523 TTATCAAAATTT-ATAATGAGA
1 TTATCAAAATTTCATAGTGTGG
* *
47544 TTAACAAAATTTGATAGTGTGG
1 TTATCAAAATTTCATAGTGTGG
* * * * *
47566 TTCTCAAAATTTTATAGGGAGA
1 TTATCAAAATTTCATAGTGTGG
** *
47588 TTAAGAAAAATTTCATAG-GTAAG
1 TT-ATCAAAATTTCATAGTGT-GG
** * **
47611 TTATCGTAATTTTAT-GCTGTAATTAA
1 TTATCAAAATTTCATAG-TG----TGG
* *
47637 TTATCAAAATTTCATTG-GGGG
1 TTATCAAAATTTCATAGTGTGG
* **
47658 TTATCAAAATTTAATAGTGTTT
1 TTATCAAAATTTCATAGTGTGG
* *
47680 TTATCAAAATTTCGTAG-GAGG
1 TTATCAAAATTTCATAGTGTGG
* * *
47701 TTAACAAAAGTT--TA-TGAGG
1 TTATCAAAATTTCATAGTGTGG
* *
47720 TTATAAAAAATTT-ATAGGGAT-G
1 TTAT-CAAAATTTCATAGTG-TGG
*
47742 TTATCAAAATTTCATAAG-ATGG
1 TTATCAAAATTTCAT-AGTGTGG
47764 TTATCAAAATTTCATGAG-GTGG
1 TTATCAAAATTTCAT-AGTGTGG
* *
47786 TTTTCAAAATTTC--A-TGAGG
1 TTATCAAAATTTCATAGTGTGG
*
47805 TTATCAAAATTTC--A-TGAGG
1 TTATCAAAATTTCATAGTGTGG
* * *
47824 TTATCAAAATTTGA-AATGGAGG
1 TTATCAAAATTTCATAGT-GTGG
* *
47846 TTATCAAAATGTT-ATAGGGAGG
1 TTATCAAAAT-TTCATAGTGTGG
* *
47868 TTTATAAAAAATTTCATAGTGAGG
1 -TTAT-CAAAATTTCATAGTGTGG
* * * *
47892 -TATCACAATTTCATGGTATGT
1 TTATCAAAATTTCATAGTGTGG
* *
47913 TTATCAAAATTTCATAATGTGA
1 TTATCAAAATTTCATAGTGTGG
* * * * *
47935 TTACCAATATTTTATCG-GAAGG
1 TTATCAAAATTTCATAGTG-TGG
* * *
47957 -TACCAAAATATCATAATGTGCG
1 TTATCAAAATTTCATAGTGTG-G
* * *
47979 CTTACCAACATTTCA-A-TGGGAG
1 -TTATCAAAATTTCATAGTGTG-G
* *
48001 TTAATCAAAATTTCATAGGGTAG
1 TT-ATCAAAATTTCATAGTGTGG
48024 TTATCAAAATTTCATTAG-GTGG
1 TTATCAAAATTTCA-TAGTGTGG
* *
48046 TTGTTAAAATTT
1 TTATCAAAATTT
48058 TGATTAGGGA
Statistics
Matches: 453, Mismatches: 116, Indels: 98
0.68 0.17 0.15
Matches are distributed among these distances:
15 8 0.02
16 1 0.00
19 44 0.10
20 8 0.02
21 86 0.19
22 222 0.49
23 36 0.08
24 32 0.07
25 1 0.00
26 13 0.03
27 2 0.00
ACGTcount: A:0.36, C:0.08, G:0.17, T:0.38
Consensus pattern (22 bp):
TTATCAAAATTTCATAGTGTGG
Found at i:47484 original size:61 final size:60
Alignment explanation
Indices: 47403--47519 Score: 155
Period size: 61 Copynumber: 1.9 Consensus size: 60
47393 GGTTATTGAA
* *
47403 ATTTTAGAGGGGAGATTATCAAAATTTCATAGTGTGGTTA-TCAAAATTTTATAATGTGGT
1 ATTTCAGAGGGGAGATTATCAAAATTTCATAGTGTGG-TAGTCAAAATTTCATAATGTGGT
* * * *
47463 ATTTCAGAGGGAGAGATTATCAAATTTTCATTGTTTGGTAGTTAAAATTTCATAATG
1 ATTTCAGAGGG-GAGATTATCAAAATTTCATAGTGTGGTAGTCAAAATTTCATAATG
47520 AGTTTATCAA
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
60 12 0.24
61 37 0.76
ACGTcount: A:0.33, C:0.06, G:0.21, T:0.40
Consensus pattern (60 bp):
ATTTCAGAGGGGAGATTATCAAAATTTCATAGTGTGGTAGTCAAAATTTCATAATGTGGT
Found at i:47538 original size:21 final size:22
Alignment explanation
Indices: 47506--47555 Score: 75
Period size: 21 Copynumber: 2.3 Consensus size: 22
47496 TTTGGTAGTT
* *
47506 AAAATTTCATAATGAGTTTATC
1 AAAATTTCATAATGAGATTAAC
47528 AAAATTT-ATAATGAGATTAAC
1 AAAATTTCATAATGAGATTAAC
47549 AAAATTT
1 AAAATTT
47556 GATAGTGTGG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
21 19 0.73
22 7 0.27
ACGTcount: A:0.48, C:0.06, G:0.08, T:0.38
Consensus pattern (22 bp):
AAAATTTCATAATGAGATTAAC
Found at i:47728 original size:19 final size:19
Alignment explanation
Indices: 47697--47734 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
47687 AATTTCGTAG
*
47697 GAGGTTAACAAAAGTTTAT
1 GAGGTTAACAAAAATTTAT
47716 GAGGTTATA-AAAAATTTAT
1 GAGGTTA-ACAAAAATTTAT
47735 AGGGATGTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 16 0.94
20 1 0.06
ACGTcount: A:0.45, C:0.03, G:0.18, T:0.34
Consensus pattern (19 bp):
GAGGTTAACAAAAATTTAT
Found at i:47781 original size:63 final size:61
Alignment explanation
Indices: 47637--47924 Score: 196
Period size: 63 Copynumber: 4.5 Consensus size: 61
47627 CTGTAATTAA
* * *** *
47637 TTATCAAAATTTCATTGGGGGTTATCAAAATTTAATAGTGTTTTTATCAAAATTTCGTAGGAGG
1 TTATCAAAATTTCA-T-GAGGTTATCAAAATTTAATAGGGAGGTTATCAAAATTTCATA-GAGG
* * *
47701 TTAACAAAAGTTT-ATGAGGTTATAAAAAATTT-ATAGGGATGTTATCAAAATTTCATAAGATGG
1 TTATCAAAA-TTTCATGAGGTTAT-CAAAATTTAATAGGGAGGTTATCAAAATTTCAT-AGA-GG
* *
47764 TTATCAAAATTTCATGAGGTGGTTTTCAAAATTTCAT---GAGGTTATCAAAATTTCAT-GAGG
1 TTATCAAAATTTCATGA---GGTTATCAAAATTTAATAGGGAGGTTATCAAAATTTCATAGAGG
* *
47824 TTATCAAAATTTGAAATGGAGGTTATCAAAATGTT-ATAGGGAGGTTTATAAAAAATTTCATAGT
1 TTATCAAAATTT--CAT-GAGGTTATCAAAAT-TTAATAGGGAGG-TTAT-CAAAATTTCATA--
47888 GAGG
58 GAGG
* *
47892 -TATCACAATTTCATGGTATGTTTATCAAAATTT
1 TTATCAAAATTTCAT-G-A-GGTTATCAAAATTT
47925 CATAATGTGA
Statistics
Matches: 184, Mismatches: 17, Indels: 44
0.75 0.07 0.18
Matches are distributed among these distances:
60 27 0.15
61 4 0.02
62 34 0.18
63 47 0.26
64 13 0.07
65 24 0.13
66 10 0.05
67 21 0.11
68 4 0.02
ACGTcount: A:0.37, C:0.07, G:0.18, T:0.38
Consensus pattern (61 bp):
TTATCAAAATTTCATGAGGTTATCAAAATTTAATAGGGAGGTTATCAAAATTTCATAGAGG
Found at i:47809 original size:41 final size:40
Alignment explanation
Indices: 47637--47855 Score: 175
Period size: 41 Copynumber: 5.2 Consensus size: 40
47627 CTGTAATTAA
*
47637 TTATCAAAATTTCATTG-GGGGTTATCAAAATTTAAT-AGTG
1 TTATCAAAATTTCA-TGAGGGGTTATCAAAATTTCATGAG-G
* *
47677 TTTTTATCAAAATTTCGT-AGGAGGTTAACAAAAGTTT-ATGAGG
1 ---TTATCAAAATTTCATGAGG-GGTTATCAAAA-TTTCATGAGG
*
47720 TTATAAAAAATTT-AT-AGGGATGTTATCAAAATTTCATAAGATGG
1 TTAT-CAAAATTTCATGAGGG--GTTATCAAAATTTCAT--GA-GG
*
47764 TTATCAAAATTTCATGAGGTGGTTTTCAAAATTTCATGAGG
1 TTATCAAAATTTCATGAGG-GGTTATCAAAATTTCATGAGG
*
47805 TTATCAAAATTTCATGA--GGTTATCAAAATTTGAAATGGAGG
1 TTATCAAAATTTCATGAGGGGTTATCAAAATTT--CAT-GAGG
47846 TTATCAAAAT
1 TTATCAAAAT
47856 GTTATAGGGA
Statistics
Matches: 150, Mismatches: 9, Indels: 36
0.77 0.05 0.18
Matches are distributed among these distances:
38 13 0.09
39 1 0.01
40 13 0.09
41 51 0.34
42 5 0.03
43 35 0.23
44 28 0.19
45 3 0.02
46 1 0.01
ACGTcount: A:0.37, C:0.07, G:0.18, T:0.37
Consensus pattern (40 bp):
TTATCAAAATTTCATGAGGGGTTATCAAAATTTCATGAGG
Found at i:47870 original size:82 final size:88
Alignment explanation
Indices: 47741--47929 Score: 202
Period size: 82 Copynumber: 2.2 Consensus size: 88
47731 TTATAGGGAT
* *
47741 GTTATCAAAATTTCATAAGATGGTTATCAAAATTTCATGAGGTGGTTT-T-CAAAATTTC-A-TG
1 GTTATCAAAATTTCATAAGATGGTTATCAAAATTTCATGAGGAGGTTTATAAAAAATTTCAAGTG
47802 AGGTTATCAAAATTTCAT-G-A-G
66 AGG-TATCAAAATTTCATGGTATG
*
47823 GTTATCAAAATTTGA-AATGGA-GGTTATCAAAATGTT-AT-AGGGAGGTTTATAAAAAATTTCA
1 GTTATCAAAATTTCATAA--GATGGTTATCAAAAT-TTCATGA-GGAGGTTTATAAAAAATTTCA
*
47884 TAGTGAGGTATCACAATTTCATGGTATG
62 -AGTGAGGTATCAAAATTTCATGGTATG
*
47912 TTTATCAAAATTTCATAA
1 GTTATCAAAATTTCATAA
47930 TGTGATTACC
Statistics
Matches: 88, Mismatches: 6, Indels: 18
0.79 0.05 0.16
Matches are distributed among these distances:
81 3 0.03
82 35 0.40
83 5 0.06
84 8 0.09
86 14 0.16
87 6 0.07
88 1 0.01
89 14 0.16
90 2 0.02
ACGTcount: A:0.37, C:0.08, G:0.17, T:0.37
Consensus pattern (88 bp):
GTTATCAAAATTTCATAAGATGGTTATCAAAATTTCATGAGGAGGTTTATAAAAAATTTCAAGTG
AGGTATCAAAATTTCATGGTATG
Found at i:47878 original size:149 final size:147
Alignment explanation
Indices: 47640--47927 Score: 338
Period size: 149 Copynumber: 1.9 Consensus size: 147
47630 TAATTAATTA
* *
47640 TCAAAATTTCATTGGGGGTTATCAAAATTTAATAGTGTTTTTATCAAAATTTCGTAGGAGGTTAA
1 TCAAAATTTCATTGGAGGTTATCAAAATTTAATAGTG--TTTATCAAAATTTCGAAGGAGGTTAA
* *
47705 CAAAAGTTTATGAGGTTATAAAAAATTT-ATAGGGATGTTATCAAAATTTCATAAG-ATGGTTAT
64 CAAAAGTTTAGGAGGTTATAAAAAATTTCATAGGGA-GGTATCAAAATTTCAT-AGTATGGTTAT
47768 CAAAATTTCATGAGGTGGTTT
127 CAAAATTTCATGAGGTGGTTT
*
47789 TCAAAATTTCA-T-GAGGTTATCAAAATTTCATGAG-G-TTATCAAAATTT-GAAATGGAGGTTA
1 TCAAAATTTCATTGGAGGTTATCAAAATTTAAT-AGTGTTTATCAAAATTTCG-AA-GGAGGTTA
* * * * *
47849 TCAAAATGTTATAGGGAGGTTTATAAAAAATTTCATAGTGAGGTATCACAATTTCATGGTATGTT
63 ACAAAA-GTT-TA-GGAGG-TTATAAAAAATTTCATAGGGAGGTATCAAAATTTCATAGTATGGT
47914 TATCAAAATTTCAT
124 TATCAAAATTTCAT
47928 AATGTGATTA
Statistics
Matches: 120, Mismatches: 10, Indels: 18
0.81 0.07 0.12
Matches are distributed among these distances:
143 1 0.01
144 13 0.11
145 13 0.11
146 3 0.03
147 20 0.17
148 8 0.07
149 56 0.47
150 6 0.05
ACGTcount: A:0.37, C:0.08, G:0.18, T:0.38
Consensus pattern (147 bp):
TCAAAATTTCATTGGAGGTTATCAAAATTTAATAGTGTTTATCAAAATTTCGAAGGAGGTTAACA
AAAGTTTAGGAGGTTATAAAAAATTTCATAGGGAGGTATCAAAATTTCATAGTATGGTTATCAAA
ATTTCATGAGGTGGTTT
Found at i:48211 original size:20 final size:21
Alignment explanation
Indices: 48147--48213 Score: 75
Period size: 22 Copynumber: 3.1 Consensus size: 21
48137 TATCGTCATA
* *
48147 AAAACTTTATAGTGTAATTATA
1 AAAATTTTATAGTG-AATTATC
48169 AAAATTTTATA-TGAAGGTTATC
1 AAAATTTTATAGTGAA--TTATC
48191 AAAATTTTATAGTG-ATTATC
1 AAAATTTTATAGTGAATTATC
48211 AAA
1 AAA
48214 TTTCATAAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
20 10 0.25
21 2 0.05
22 26 0.65
23 2 0.05
ACGTcount: A:0.45, C:0.04, G:0.10, T:0.40
Consensus pattern (21 bp):
AAAATTTTATAGTGAATTATC
Found at i:50081 original size:32 final size:32
Alignment explanation
Indices: 50028--50090 Score: 83
Period size: 32 Copynumber: 2.0 Consensus size: 32
50018 TGAATTTTTT
*
50028 AAAATTAAAAAGTCATGTTCATACAATTGCCG
1 AAAATTAAAAAGTCATATTCATACAATTGCCG
* *
50060 AAAATT-AAAATTCCATATTCATACAGTTGCC
1 AAAATTAAAAAGT-CATATTCATACAATTGCC
50091 AGCACCTAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
31 5 0.19
32 22 0.81
ACGTcount: A:0.43, C:0.17, G:0.10, T:0.30
Consensus pattern (32 bp):
AAAATTAAAAAGTCATATTCATACAATTGCCG
Done.