Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021363.1 Corchorus olitorius cultivar O-4 contig21396, 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: 72470
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Found at i:1007 original size:4 final size:4
Alignment explanation
Indices: 996--1273 Score: 94
Period size: 4 Copynumber: 72.0 Consensus size: 4
986 GAATTTTTTT
* *
996 TTTA -TTA TTTA TTTA -CTA TTTA TTT- TTTA TTT- TTTA TTTTT TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA -TTTA TTTA
* * * * * *
1041 TTT- TTACA TTT- TTAA CTATTA TCTA TTTA TTCA -CTA TTTA TCTA TTTA
1 TTTA TT-TA TTTA TTTA -T-TTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
* * * * ** *
1089 TTTA -CTA TTTA CTTTT TTTA -TTA TCTA CTTA TTTA -CCA TTTA TCTA
1 TTTA TTTA TTTA -TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
* * *
1135 TTTA TTTA TTT- TTAA CTATTA TCTA TTTA TTTA -CTA TTTA TCTT- TTTA
1 TTTA TTTA TTTA TTTA -T-TTA TTTA TTTA TTTA TTTA TTTA T-TTA TTTA
* **
1183 TTTA -TT- TTTA ATTA -TTA CCTA TTTA TTACTA TTTA TCTT- TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT--TA TTTA T-TTA TTTA TTTA
* * *
1230 TTAA TTTA GTTA -TTA TCTA TTTA TTTA TTTA -TTA -TTA TTT- TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
1274 GCTACCTATT
Statistics
Matches: 198, Mismatches: 45, Indels: 62
0.65 0.15 0.20
Matches are distributed among these distances:
3 49 0.25
4 125 0.63
5 16 0.08
6 8 0.04
ACGTcount: A:0.25, C:0.08, G:0.00, T:0.67
Consensus pattern (4 bp):
TTTA
Found at i:1008 original size:7 final size:7
Alignment explanation
Indices: 1004--1265 Score: 73
Period size: 7 Copynumber: 36.7 Consensus size: 7
994 TTTTTATTAT
1004 TTATTTA
1 TTATTTA
*
1011 CTATTTA
1 TTATTTA
*
1018 TTTTTTA
1 TTATTTA
*
1025 TTTTTTA
1 TTATTTA
*
1032 TT-TTTT
1 TTATTTA
1038 TTATTT-
1 TTATTTA
1044 TTACATTT-
1 TT--ATTTA
**
1052 TTAACTA
1 TTATTTA
*
1059 TTATCTA
1 TTATTTA
*
1066 TTTATTCA
1 -TTATTTA
*
1074 CTATTTA
1 TTATTTA
1081 TCTA--T-
1 T-TATTTA
1086 TTATTTA
1 TTATTTA
*
1093 CTATTTA
1 TTATTTA
*
1100 CTTTTTTTA
1 --TTATTTA
*
1109 TTATCTA
1 TTATTTA
1116 CTTATTTA
1 -TTATTTA
**
1124 CCATTTA
1 TTATTTA
1131 TCTATTTA
1 T-TATTTA
1139 TTTATTT-
1 -TTATTTA
**
1146 TTAACTA
1 TTATTTA
*
1153 TTATCTA
1 TTATTTA
1160 TTTATTTA
1 -TTATTTA
*
1168 CTATTTA
1 TTATTTA
*
1175 -TCTTT-
1 TTATTTA
1180 TTATTTA
1 TTATTTA
1187 TT-TTTAA
1 TTATTT-A
1194 TTA-TTA
1 TTATTTA
*
1200 CCTATTTA
1 -TTATTTA
*
1208 TTA-CTA
1 TTATTTA
*
1214 TTTATCTTT
1 -TTAT-TTA
1223 TTATTTA
1 TTATTTA
1230 TTAATTTA
1 TT-ATTTA
1238 GTTA-TTA
1 -TTATTTA
1245 TCTATTTA
1 T-TATTTA
1253 TTTATTTA
1 -TTATTTA
1261 TTATT
1 TTATT
1266 ATTTTTTAGC
Statistics
Matches: 190, Mismatches: 35, Indels: 60
0.67 0.12 0.21
Matches are distributed among these distances:
4 2 0.01
5 1 0.01
6 30 0.16
7 90 0.47
8 57 0.30
9 10 0.05
ACGTcount: A:0.25, C:0.09, G:0.00, T:0.66
Consensus pattern (7 bp):
TTATTTA
Found at i:1031 original size:14 final size:14
Alignment explanation
Indices: 988--1037 Score: 57
Period size: 14 Copynumber: 3.5 Consensus size: 14
978 ACCCAAAAGA
988 ATTTTTT-TTTTATT
1 ATTTTTTATTTT-TT
* *
1002 ATTTATTTACTATTT
1 ATTT-TTTATTTTTT
1017 ATTTTTTATTTTTT
1 ATTTTTTATTTTTT
1031 ATTTTTT
1 ATTTTTT
1038 TTATTTTTAC
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
14 19 0.63
15 9 0.30
16 2 0.07
ACGTcount: A:0.18, C:0.02, G:0.00, T:0.80
Consensus pattern (14 bp):
ATTTTTTATTTTTT
Found at i:1165 original size:44 final size:44
Alignment explanation
Indices: 1075--1256 Score: 228
Period size: 44 Copynumber: 4.1 Consensus size: 44
1065 ATTTATTCAC
** *
1075 TATTTATCTATTTAT-TTACTATTTACTTTTT--TTATTATCTACT
1 TATTTA-CTATTTATCTTTTTATTTA-TTTTTAATTATTATCTATT
* * *
1118 TATTTACCATTTATCTATTTATTTATTTTTAACTATTATCTATT
1 TATTTACTATTTATCTTTTTATTTATTTTTAATTATTATCTATT
*
1162 TATTTACTATTTATCTTTTTATTTATTTTTAATTATTACCTATT
1 TATTTACTATTTATCTTTTTATTTATTTTTAATTATTATCTATT
*
1206 TA-TTACTATTTATCTTTTTATTTATTAATTTAGTTATTATCTATT
1 TATTTACTATTTATCTTTTTATTTATT--TTTAATTATTATCTATT
1251 TATTTA
1 TATTTA
1257 TTTATTATTA
Statistics
Matches: 121, Mismatches: 12, Indels: 9
0.85 0.08 0.06
Matches are distributed among these distances:
42 12 0.10
43 37 0.31
44 52 0.43
45 17 0.14
46 3 0.02
ACGTcount: A:0.26, C:0.09, G:0.01, T:0.64
Consensus pattern (44 bp):
TATTTACTATTTATCTTTTTATTTATTTTTAATTATTATCTATT
Found at i:1185 original size:19 final size:19
Alignment explanation
Indices: 1055--1186 Score: 96
Period size: 19 Copynumber: 7.1 Consensus size: 19
1045 TACATTTTTA
* *
1055 ACTA-TTATCTATTTATTC
1 ACTATTTATCTTTTTATTT
*
1073 ACTATTTATCTATTTATTT
1 ACTATTTATCTTTTTATTT
*
1092 ACTATTTA-CTTTTTTTATT
1 ACTATTTATCTTTTTAT-TT
* ***
1111 ATCTACTTAT-TTACCATTT
1 A-CTATTTATCTTTTTATTT
*
1130 ATCTATTTAT-TTATTT-TTA
1 A-CTATTTATCTT-TTTATTT
*
1149 ACTA-TTATCTATTTATTT
1 ACTATTTATCTTTTTATTT
1167 ACTATTTATCTTTTTATTT
1 ACTATTTATCTTTTTATTT
1186 A
1 A
1187 TTTTTAATTA
Statistics
Matches: 90, Mismatches: 16, Indels: 15
0.74 0.13 0.12
Matches are distributed among these distances:
17 7 0.08
18 20 0.22
19 54 0.60
20 9 0.10
ACGTcount: A:0.26, C:0.12, G:0.00, T:0.62
Consensus pattern (19 bp):
ACTATTTATCTTTTTATTT
Found at i:1216 original size:94 final size:90
Alignment explanation
Indices: 1035--1256 Score: 238
Period size: 94 Copynumber: 2.4 Consensus size: 90
1025 TTTTTTATTT
*
1035 TTTTTATTT-TTACATTTTTAACTATTATCTATTTATTCACTATTTATCTATTTATTTACTATTT
1 TTTTTATTTATT--ATTTTTAACTATTATCTATTTATTTACTATTTATCTATTTATTTACTATTT
* **
1099 ACTTTTTTTATTATCTACTTATTTACC
64 AATTTTCCTATTATCTACTTATTTACC
* *
1126 ATTTATCTATTTATTTATTTTTAACTATTATCTATTTATTTACTATTTATCTTTTTATTTA-TTT
1 -TTT-T-TATTTA-TTATTTTTAACTATTATCTATTTATTTACTATTTATCTATTTATTTACTAT
*
1190 TTAATTATTACCTATTTAT-TAC-TATTTATC
62 TTAATT-TT-CCTA-TTATCTACTTATTTACC
* **
1220 TTTTTATTTATTA-ATTTAGTTATTATCTATTTATTTA
1 TTTTTATTTATTATTTTTAACTATTATCTATTTATTTA
1257 TTTATTATTA
Statistics
Matches: 113, Mismatches: 10, Indels: 17
0.81 0.07 0.12
Matches are distributed among these distances:
89 21 0.19
90 3 0.03
91 6 0.05
92 4 0.04
93 11 0.10
94 57 0.50
95 5 0.04
96 6 0.05
ACGTcount: A:0.26, C:0.10, G:0.00, T:0.64
Consensus pattern (90 bp):
TTTTTATTTATTATTTTTAACTATTATCTATTTATTTACTATTTATCTATTTATTTACTATTTAA
TTTTCCTATTATCTACTTATTTACC
Found at i:1250 original size:19 final size:18
Alignment explanation
Indices: 1227--1268 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 18
1217 ATCTTTTTAT
1227 TTATTAATTTAGTTATTA
1 TTATTAATTTAGTTATTA
* *
1245 TCTATTTATTTATTTATTA
1 T-TATTAATTTAGTTATTA
1264 TTATT
1 TTATT
1269 TTTTAGCTAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 5 0.24
19 16 0.76
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (18 bp):
TTATTAATTTAGTTATTA
Found at i:8393 original size:17 final size:17
Alignment explanation
Indices: 8371--8403 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
8361 TTTGCCTTGC
8371 CATTTAGAACTCTGCTG
1 CATTTAGAACTCTGCTG
*
8388 CATTTAGAATTCTGCT
1 CATTTAGAACTCTGCT
8404 TTCTGAGTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.24, C:0.21, G:0.15, T:0.39
Consensus pattern (17 bp):
CATTTAGAACTCTGCTG
Found at i:9428 original size:29 final size:29
Alignment explanation
Indices: 9387--9621 Score: 301
Period size: 29 Copynumber: 8.1 Consensus size: 29
9377 GAATAAAACC
9387 AAAATGACCAAAATGCCCCTGGATGTGCA
1 AAAATGACCAAAATGCCCCTGGATGTGCA
* *
9416 AAAATGACTAAAATGCCCCTAGATGTGCA
1 AAAATGACCAAAATGCCCCTGGATGTGCA
* *
9445 AAAATGACCAAAATGCCCCCGGATATGC-
1 AAAATGACCAAAATGCCCCTGGATGTGCA
* *
9473 AAAATAACCAAAATGCCCCTGAATGTGCA
1 AAAATGACCAAAATGCCCCTGGATGTGCA
* * *
9502 AAAATAACCAAAATGCCCCTGAATATGCA
1 AAAATGACCAAAATGCCCCTGGATGTGCA
* * * * *
9531 AAGATGACCATAATGCCCTTGGATGGGTA
1 AAAATGACCAAAATGCCCCTGGATGTGCA
* * *
9560 AAAATGACCAAAATGCCCTTGGATGGGTA
1 AAAATGACCAAAATGCCCCTGGATGTGCA
*
9589 AAAATGACCAAAATGCCCCTGGATATGCA
1 AAAATGACCAAAATGCCCCTGGATGTGCA
9618 AAAA
1 AAAA
9622 GGTCAATTAA
Statistics
Matches: 180, Mismatches: 25, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
28 24 0.13
29 156 0.87
ACGTcount: A:0.41, C:0.22, G:0.18, T:0.18
Consensus pattern (29 bp):
AAAATGACCAAAATGCCCCTGGATGTGCA
Found at i:9531 original size:86 final size:87
Alignment explanation
Indices: 9386--9621 Score: 305
Period size: 86 Copynumber: 2.7 Consensus size: 87
9376 AGAATAAAAC
* *
9386 CAAAATGACCAAAATGCCCCTGGATGTGCAAAAATGACTAAAATGCCCCT-AGATGTGCAAAAAT
1 CAAAATGACCAAAATGCCCCTGGATGTGCAAAAATGACCAAAATGCCCCTGA-ATATGCAAAAAT
*
9450 GACCAAAATGCCCCCGGATATG-
65 GACCAAAATGCCCCCGGATAGGT
* * * *
9472 CAAAATAACCAAAATGCCCCTGAATGTGCAAAAATAACCAAAATGCCCCTGAATATGCAAAGATG
1 CAAAATGACCAAAATGCCCCTGGATGTGCAAAAATGACCAAAATGCCCCTGAATATGCAAAAATG
* ** *
9537 ACCATAATGCCCTTGGATGGGT
66 ACCAAAATGCCCCCGGATAGGT
* * * * *
9559 AAAAATGACCAAAATGCCCTTGGATGGGTAAAAATGACCAAAATGCCCCTGGATATGCAAAAA
1 CAAAATGACCAAAATGCCCCTGGATGTGCAAAAATGACCAAAATGCCCCTGAATATGCAAAAA
9622 GGTCAATTAA
Statistics
Matches: 128, Mismatches: 20, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
86 73 0.57
87 55 0.43
ACGTcount: A:0.41, C:0.22, G:0.18, T:0.18
Consensus pattern (87 bp):
CAAAATGACCAAAATGCCCCTGGATGTGCAAAAATGACCAAAATGCCCCTGAATATGCAAAAATG
ACCAAAATGCCCCCGGATAGGT
Found at i:10365 original size:31 final size:30
Alignment explanation
Indices: 10327--10431 Score: 99
Period size: 31 Copynumber: 3.5 Consensus size: 30
10317 TAAGGCTAAT
10327 TGCTCAAATAAGGGCCTAACGTTTGCCAAAA
1 TGCTCAAATAAGGGCCTAACGTTT-CCAAAA
* * **
10358 TGCTCAAATAAGGGCCCAATC-TTT-TAATT
1 TGCTCAAATAAGGGCCTAA-CGTTTCCAAAA
*
10387 TGGC-CAAATAAGGGCCTAACGTTATCGAAAA
1 T-GCTCAAATAAGGGCCTAACGTT-TCCAAAA
*
10418 TGCTTAAATAAGGG
1 TGCTCAAATAAGGG
10432 TCCGATCTTT
Statistics
Matches: 59, Mismatches: 9, Indels: 12
0.74 0.11 0.15
Matches are distributed among these distances:
28 1 0.02
29 19 0.32
30 5 0.08
31 33 0.56
32 1 0.02
ACGTcount: A:0.35, C:0.19, G:0.20, T:0.26
Consensus pattern (30 bp):
TGCTCAAATAAGGGCCTAACGTTTCCAAAA
Found at i:10427 original size:60 final size:61
Alignment explanation
Indices: 10331--10492 Score: 229
Period size: 60 Copynumber: 2.7 Consensus size: 61
10321 GCTAATTGCT
* *
10331 CAAATAAGGGCCTAACGTT-TGCCAAAATGCTCAAATAAGGGCCCAATCTTTTAATTTGGC
1 CAAATAAGGGCCTAACGTTATACAAAAATGCTCAAATAAGGGCCCAATCTTTTAATTTGGC
* * * *
10391 CAAATAAGGGCCTAACGTTAT-CGAAAATGCTTAAATAAGGGTCCGATCTTTTAATTTGGC
1 CAAATAAGGGCCTAACGTTATACAAAAATGCTCAAATAAGGGCCCAATCTTTTAATTTGGC
** *
10451 CAAATAAGGATCTAACGTTATAAAAAAATGCTCAAATAAGGG
1 CAAATAAGGGCCTAACGTTATACAAAAATGCTCAAATAAGGG
10493 TCTGGCGTCA
Statistics
Matches: 91, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
60 73 0.80
61 18 0.20
ACGTcount: A:0.38, C:0.17, G:0.19, T:0.27
Consensus pattern (61 bp):
CAAATAAGGGCCTAACGTTATACAAAAATGCTCAAATAAGGGCCCAATCTTTTAATTTGGC
Found at i:10572 original size:31 final size:30
Alignment explanation
Indices: 10534--10701 Score: 141
Period size: 31 Copynumber: 5.6 Consensus size: 30
10524 TTTCAATGCC
10534 AGGCCCTTATTTGAGCATTTTGGCAAACGTT
1 AGGCCCTTATTTGAGCATTTT-GCAAACGTT
* ** * *
10565 AGGCCCTTAATTG-GCCAAATT--AAAAGATC
1 AGGCCCTTATTTGAG-CATTTTGCAAACG-TT
*
10594 AGGCCTTTATTTGAGCATTTTGGCAAACGTT
1 AGGCCCTTATTTGAGCATTTT-GCAAACGTT
** * *
10625 AGGCCCTTATTTG-GCCAAATT--AAAAGATC
1 AGGCCCTTATTTGAG-CATTTTGCAAACG-TT
10654 AGGCCCTTATTTGAGCATTTTGACAAACGTT
1 AGGCCCTTATTTGAGCATTTTG-CAAACGTT
10685 AGGCCCTTATTTGAGCA
1 AGGCCCTTATTTGAGCA
10702 ACTAGCCTAA
Statistics
Matches: 105, Mismatches: 20, Indels: 24
0.70 0.13 0.16
Matches are distributed among these distances:
28 8 0.08
29 34 0.32
30 4 0.04
31 51 0.49
32 8 0.08
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.32
Consensus pattern (30 bp):
AGGCCCTTATTTGAGCATTTTGCAAACGTT
Found at i:10660 original size:29 final size:29
Alignment explanation
Indices: 10565--10666 Score: 100
Period size: 29 Copynumber: 3.4 Consensus size: 29
10555 GGCAAACGTT
*
10565 AGGCCCTTAATTGGCCAAATTAAAAGATC
1 AGGCCCTTATTTGGCCAAATTAAAAGATC
* ** * *
10594 AGGCCTTTATTTGAG-CATTTTGGCAAACG-TT
1 AGGCCCTTATTTG-GCCAAATT---AAAAGATC
10625 AGGCCCTTATTTGGCCAAATTAAAAGATC
1 AGGCCCTTATTTGGCCAAATTAAAAGATC
10654 AGGCCCTTATTTG
1 AGGCCCTTATTTG
10667 AGCATTTTGA
Statistics
Matches: 56, Mismatches: 11, Indels: 12
0.71 0.14 0.15
Matches are distributed among these distances:
28 4 0.07
29 29 0.52
30 2 0.04
31 17 0.30
32 4 0.07
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.31
Consensus pattern (29 bp):
AGGCCCTTATTTGGCCAAATTAAAAGATC
Found at i:10694 original size:60 final size:60
Alignment explanation
Indices: 10533--10697 Score: 303
Period size: 60 Copynumber: 2.8 Consensus size: 60
10523 TTTTCAATGC
*
10533 CAGGCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTAATTGGCCAAATTAAAAGAT
1 CAGGCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGAT
*
10593 CAGGCCTTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGAT
1 CAGGCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGAT
*
10653 CAGGCCCTTATTTGAGCATTTTGACAAACGTTAGGCCCTTATTTG
1 CAGGCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTG
10698 AGCAACTAGC
Statistics
Matches: 101, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
60 101 1.00
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33
Consensus pattern (60 bp):
CAGGCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGAT
Found at i:11024 original size:17 final size:17
Alignment explanation
Indices: 10976--11024 Score: 71
Period size: 17 Copynumber: 2.9 Consensus size: 17
10966 TCAAATTATT
* *
10976 TCGGGTTCGAGCTCAGG
1 TCGGGTTCGGGCTCGGG
*
10993 TCGGGATCGGGCTCGGG
1 TCGGGTTCGGGCTCGGG
11010 TCGGGTTCGGGCTCG
1 TCGGGTTCGGGCTCG
11025 ATCTGCCTCG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.06, C:0.24, G:0.47, T:0.22
Consensus pattern (17 bp):
TCGGGTTCGGGCTCGGG
Found at i:12000 original size:36 final size:36
Alignment explanation
Indices: 11960--12028 Score: 120
Period size: 36 Copynumber: 1.9 Consensus size: 36
11950 TATGAAGAAT
*
11960 TTAAATGGAAAATTAAATATAAGTATTTAGTATACG
1 TTAAAAGGAAAATTAAATATAAGTATTTAGTATACG
*
11996 TTAAAAGGAAAGTTAAATATAAGTATTTAGTAT
1 TTAAAAGGAAAATTAAATATAAGTATTTAGTAT
12029 TATGCCCTCT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.48, C:0.01, G:0.14, T:0.36
Consensus pattern (36 bp):
TTAAAAGGAAAATTAAATATAAGTATTTAGTATACG
Found at i:23188 original size:2 final size:2
Alignment explanation
Indices: 23181--23238 Score: 98
Period size: 2 Copynumber: 29.0 Consensus size: 2
23171 AATATAGCTC
* *
23181 AT AT AT AT AT AT AC AT AT AC AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
23223 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
23239 CTTACAAGAA
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:33302 original size:140 final size:140
Alignment explanation
Indices: 33050--33330 Score: 544
Period size: 140 Copynumber: 2.0 Consensus size: 140
33040 CTTTACCACT
*
33050 ATCCATTTTGACACCATCACCCGAAACAACATACCCCAAAAATGCAATTTCATGAGTGAAGAAAT
1 ATCCATTTTGACACCATCACCCGAAACAACATACCCCAAAAATGCAACTTCATGAGTGAAGAAAT
33115 GGCACTTCTTCACATTGGCATAAAGCTTCTCATTTCTCAACAAATCAAACACTTTTCTCAAATGC
66 GGCACTTCTTCACATTGGCATAAAGCTTCTCATTTCTCAACAAATCAAACACTTTTCTCAAATGC
33180 ACAAGATGAG
131 ACAAGATGAG
*
33190 ATCCATTTTGACACCATCACCCGAAACAACATACCCCGAAAATGCAACTTCATGAGTGAAGAAAT
1 ATCCATTTTGACACCATCACCCGAAACAACATACCCCAAAAATGCAACTTCATGAGTGAAGAAAT
33255 GGCACTTCTTCACATTGGCATAAAGCTTCTCATTTCTCAACAAATCAAACACTTTTCTCAAATGC
66 GGCACTTCTTCACATTGGCATAAAGCTTCTCATTTCTCAACAAATCAAACACTTTTCTCAAATGC
33320 ACAAGATGAG
131 ACAAGATGAG
33330 A
1 A
33331 ATCTTCATCA
Statistics
Matches: 139, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
140 139 1.00
ACGTcount: A:0.37, C:0.26, G:0.12, T:0.25
Consensus pattern (140 bp):
ATCCATTTTGACACCATCACCCGAAACAACATACCCCAAAAATGCAACTTCATGAGTGAAGAAAT
GGCACTTCTTCACATTGGCATAAAGCTTCTCATTTCTCAACAAATCAAACACTTTTCTCAAATGC
ACAAGATGAG
Found at i:42505 original size:2 final size:2
Alignment explanation
Indices: 42498--42527 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
42488 ATTTATGGTA
42498 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
42528 CATGCACATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:44905 original size:28 final size:28
Alignment explanation
Indices: 44872--44929 Score: 91
Period size: 28 Copynumber: 2.1 Consensus size: 28
44862 TTTGTTTCTA
*
44872 TTTGCAATTAATGACTTGCAA-ATTTGTC
1 TTTGCAATTAATCACTTGCAATA-TTGTC
44900 TTTGCAATTAATCACTTGCAATATTGTC
1 TTTGCAATTAATCACTTGCAATATTGTC
44928 TT
1 TT
44930 CAAGCAATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
28 27 0.96
29 1 0.04
ACGTcount: A:0.28, C:0.16, G:0.12, T:0.45
Consensus pattern (28 bp):
TTTGCAATTAATCACTTGCAATATTGTC
Found at i:53993 original size:51 final size:51
Alignment explanation
Indices: 53934--54088 Score: 292
Period size: 51 Copynumber: 3.0 Consensus size: 51
53924 AGATAGGTAG
53934 GTAGTTTATTTATGGTATAGTTTCTAGTTTGGGTTGAATTCTCATTTAGAT
1 GTAGTTTATTTATGGTATAGTTTCTAGTTTGGGTTGAATTCTCATTTAGAT
53985 GTAGTTTATTTATGGTATAGTTTCTAGTTTGGGTTGAATTCTCATTTAGAT
1 GTAGTTTATTTATGGTATAGTTTCTAGTTTGGGTTGAATTCTCATTTAGAT
* *
54036 ATAGTTTATTTAAGGTATAGTTTCTAGTTTGGGTTGAATTCTCATTTAGAT
1 GTAGTTTATTTATGGTATAGTTTCTAGTTTGGGTTGAATTCTCATTTAGAT
54087 GT
1 GT
54089 TTGGATATAG
Statistics
Matches: 101, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
51 101 1.00
ACGTcount: A:0.23, C:0.06, G:0.21, T:0.50
Consensus pattern (51 bp):
GTAGTTTATTTATGGTATAGTTTCTAGTTTGGGTTGAATTCTCATTTAGAT
Found at i:57749 original size:30 final size:30
Alignment explanation
Indices: 57715--57798 Score: 123
Period size: 31 Copynumber: 2.7 Consensus size: 30
57705 TTAATTTCTA
57715 AAAATCTTCTTTTGGATTGCTTTATTTTCC
1 AAAATCTTCTTTTGGATTGCTTTATTTTCC
* * *
57745 AAAATCCTCTTTTGGAATTACCTTATTTTCC
1 AAAATCTTCTTTTGG-ATTGCTTTATTTTCC
57776 AAAATCTTCTTTTGGATTTGCTT
1 AAAATCTTCTTTTGGA-TTGCTT
57799 AAGAAAAGAT
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
30 15 0.33
31 31 0.67
ACGTcount: A:0.23, C:0.18, G:0.10, T:0.50
Consensus pattern (30 bp):
AAAATCTTCTTTTGGATTGCTTTATTTTCC
Found at i:61324 original size:23 final size:23
Alignment explanation
Indices: 61294--61384 Score: 173
Period size: 23 Copynumber: 3.9 Consensus size: 23
61284 CCTGCTTCAC
61294 TGCTTTGGGATGTTCTTGTAACT
1 TGCTTTGGGATGTTCTTGTAACT
61317 TGCTTTGGGATGTTCTTGTAACT
1 TGCTTTGGGATGTTCTTGTAACT
61340 TGCTTTGGGATGTTCTTGTAACT
1 TGCTTTGGGATGTTCTTGTAACT
61363 TGCTTTGGGATGTTCTTAGTAA
1 TGCTTTGGGATGTTCTT-GTAA
61385 AGGGAATGTA
Statistics
Matches: 67, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
23 63 0.94
24 4 0.06
ACGTcount: A:0.14, C:0.12, G:0.26, T:0.47
Consensus pattern (23 bp):
TGCTTTGGGATGTTCTTGTAACT
Found at i:63598 original size:15 final size:15
Alignment explanation
Indices: 63578--63608 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
63568 CCATTGAACA
63578 TAATTTTAATAGGTG
1 TAATTTTAATAGGTG
63593 TAATTTTAATAGGTG
1 TAATTTTAATAGGTG
63608 T
1 T
63609 TTTCCATCCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.19, T:0.48
Consensus pattern (15 bp):
TAATTTTAATAGGTG
Found at i:67289 original size:14 final size:14
Alignment explanation
Indices: 67255--67299 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
67245 ACTATAATAA
67255 TTAGTTAATTTTCTT
1 TTAGTT-ATTTTCTT
* *
67270 TAAGTTATTTTGTT
1 TTAGTTATTTTCTT
*
67284 TTAGTTATTTCCTT
1 TTAGTTATTTTCTT
67298 TT
1 TT
67300 GCACAACTCT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
14 20 0.80
15 5 0.20
ACGTcount: A:0.18, C:0.07, G:0.09, T:0.67
Consensus pattern (14 bp):
TTAGTTATTTTCTT
Found at i:68809 original size:16 final size:16
Alignment explanation
Indices: 68788--68818 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
68778 ACTGGAAGCA
*
68788 AGAAGCAAGAAGCAAG
1 AGAAGCAAAAAGCAAG
68804 AGAAGCAAAAAGCAA
1 AGAAGCAAAAAGCAA
68819 CAAGGCTGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.61, C:0.13, G:0.26, T:0.00
Consensus pattern (16 bp):
AGAAGCAAAAAGCAAG
Done.