Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168149.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_390, 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: 29296
ACGTcount: A:0.37, C:0.15, G:0.13, T:0.35
Found at i:1018 original size:33 final size:33
Alignment explanation
Indices: 956--1170 Score: 297
Period size: 33 Copynumber: 6.5 Consensus size: 33
946 TTAAGCCTAA
* * * *
956 TTATCTAGCC-TCAAATGAAGTTTTTAGCCCAGC
1 TTATCTGGCCATC-AATGAAGCTTTAAGCCCAGT
* *
989 TTATATGGCCATTAATGAAGCTTTAAGCCCAGT
1 TTATCTGGCCATCAATGAAGCTTTAAGCCCAGT
*
1022 TTATCTGGCCATCAATGAAACTTTAAGCCCAGT
1 TTATCTGGCCATCAATGAAGCTTTAAGCCCAGT
* * *
1055 TTATCTGGCCATTAATGAAGTTTTAAGTCCAGT
1 TTATCTGGCCATCAATGAAGCTTTAAGCCCAGT
*
1088 TTATCTGACCATCAATGAAGCATTTAAGCCCAGT
1 TTATCTGGCCATCAATGAAGC-TTTAAGCCCAGT
*
1122 TTATCTGGCCATAAATGAAGCTTTAAGCCCAGT
1 TTATCTGGCCATCAATGAAGCTTTAAGCCCAGT
1155 TTATCTGGCCATCAAT
1 TTATCTGGCCATCAAT
1171 AAAATTTTAA
Statistics
Matches: 160, Mismatches: 20, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
33 129 0.81
34 31 0.19
ACGTcount: A:0.29, C:0.21, G:0.16, T:0.33
Consensus pattern (33 bp):
TTATCTGGCCATCAATGAAGCTTTAAGCCCAGT
Found at i:1180 original size:33 final size:33
Alignment explanation
Indices: 941--1183 Score: 274
Period size: 33 Copynumber: 7.4 Consensus size: 33
931 AAAAAAAAAA
* * *
941 AAACTTTAAGCCTA-ATTATCTAGCC-TCAAATG
1 AAACTTTAAGCCCAGTTTATCTGGCCATC-AATG
** * * * *
973 AAGTTTTTAGCCCAGCTTATATGGCCATTAATG
1 AAACTTTAAGCCCAGTTTATCTGGCCATCAATG
*
1006 AAGCTTTAAGCCCAGTTTATCTGGCCATCAATG
1 AAACTTTAAGCCCAGTTTATCTGGCCATCAATG
*
1039 AAACTTTAAGCCCAGTTTATCTGGCCATTAATG
1 AAACTTTAAGCCCAGTTTATCTGGCCATCAATG
** * *
1072 AAGTTTTAAGTCCAGTTTATCTGACCATCAATG
1 AAACTTTAAGCCCAGTTTATCTGGCCATCAATG
* *
1105 AAGCATTTAAGCCCAGTTTATCTGGCCATAAATG
1 AAAC-TTTAAGCCCAGTTTATCTGGCCATCAATG
* *
1139 AAGCTTTAAGCCCAGTTTATCTGGCCATCAATA
1 AAACTTTAAGCCCAGTTTATCTGGCCATCAATG
*
1172 AAATTTTAAGCC
1 AAACTTTAAGCC
1184 ATTAATGAAG
Statistics
Matches: 180, Mismatches: 28, Indels: 5
0.85 0.13 0.02
Matches are distributed among these distances:
32 10 0.06
33 139 0.77
34 31 0.17
ACGTcount: A:0.31, C:0.21, G:0.15, T:0.33
Consensus pattern (33 bp):
AAACTTTAAGCCCAGTTTATCTGGCCATCAATG
Found at i:1224 original size:33 final size:33
Alignment explanation
Indices: 1181--2004 Score: 827
Period size: 33 Copynumber: 25.1 Consensus size: 33
1171 AAAATTTTAA
* *
1181 GCCATTAATGAAGTTTTAAGCCCAGTTTATCTG
1 GCCATCAATGAAGCTTTAAGCCCAGTTTATCTG
1214 GCCATCAATGAAGCATTTAAGCCCAGTTTATCTG
1 GCCATCAATGAAGC-TTTAAGCCCAGTTTATCTG
* * * *
1248 GTCATCAATGAAGTTTTAAGCCTAGTTTATCTA
1 GCCATCAATGAAGCTTTAAGCCCAGTTTATCTG
** *
1281 GCTC-TCAATGAAATTTTAAGCCCAATTTATCTG
1 GC-CATCAATGAAGCTTTAAGCCCAGTTTATCTG
* * *
1314 GCCATCAATTACGCTTTAAGCCCAATTTATCTG
1 GCCATCAATGAAGCTTTAAGCCCAGTTTATCTG
* * *
1347 GTC-TCAAATGAAGTTTTAAACCCAGTTTATCTG
1 GCCATC-AATGAAGCTTTAAGCCCAGTTTATCTG
* *
1380 GTCATCAATGAAACTTTAAGCCCAGTTTATCTG
1 GCCATCAATGAAGCTTTAAGCCCAGTTTATCTG
* * * *
1413 ACCATTAATGAAACTTTAAGCCCAGTTTATCTA
1 GCCATCAATGAAGCTTTAAGCCCAGTTTATCTG
* * *
1446 GCCATTAAT-AACGCTTTAAGCTCAATTTATCTG
1 GCCATCAATGAA-GCTTTAAGCCCAGTTTATCTG
* * *
1479 ACC-TCAAATGAAGCTTTAAGCCCAATTTATTTG
1 GCCATC-AATGAAGCTTTAAGCCCAGTTTATCTG
* *
1512 GCCATTAATGAAGCTTTAAGCCTAGTTTATCTG
1 GCCATCAATGAAGCTTTAAGCCCAGTTTATCTG
* *
1545 GCCATTAATGAAACTTTAAGCCCAGTTTATCTG
1 GCCATCAATGAAGCTTTAAGCCCAGTTTATCTG
* * * * *
1578 ACTC-TTAATGAAACTTTAAACCTAGTTTATCTG
1 GC-CATCAATGAAGCTTTAAGCCCAGTTTATCTG
*
1611 GCCATTAATGAAGCTTTAAGCCCAGTTTATCTG
1 GCCATCAATGAAGCTTTAAGCCCAGTTTATCTG
* * *
1644 ACTC-TTAATGAAACTTTAAGCCCAGTTTATCTG
1 GC-CATCAATGAAGCTTTAAGCCCAGTTTATCTG
*
1677 GCCAACAATG-A-CATTTAAGCCCAGTTTATCTG
1 GCCATCAATGAAGC-TTTAAGCCCAGTTTATCTG
* *
1709 GCCATTAATGAAGCTTTAAGCCCAGCTTATCTG
1 GCCATCAATGAAGCTTTAAGCCCAGTTTATCTG
* * *
1742 GCCATCAATGAGGCTTTAAACCCAATTTATCTG
1 GCCATCAATGAAGCTTTAAGCCCAGTTTATCTG
* * *
1775 ACC-TCAAATGAAGATTTAAGCCCAGTTTATCTT
1 GCCATC-AATGAAGCTTTAAGCCCAGTTTATCTG
*
1808 GCCCTCAATGAAGCTTTAAGCCCAGTTTATCTG
1 GCCATCAATGAAGCTTTAAGCCCAGTTTATCTG
* * *
1841 ACCAAT-AATG-A-CATTTAAACCCAGTTTGTCTG
1 GCC-ATCAATGAAGC-TTTAAGCCCAGTTTATCTG
*
1873 GCCATTAATGAAGCTTTAAG-CCAGTTTATCTG
1 GCCATCAATGAAGCTTTAAGCCCAGTTTATCTG
**
1905 GCCATCAATGATA--TTTAAATCCAGTTTATCTG
1 GCCATCAATGA-AGCTTTAAGCCCAGTTTATCTG
* * * *
1937 GCC-TCAAATGAGGATTTAAGCCCAATTTAGCTG
1 GCCATC-AATGAAGCTTTAAGCCCAGTTTATCTG
* ** * *
1970 GCCTTCAAT-AAAATTTAAGCCAAGTTTATTTG
1 GCCATCAATGAAGCTTTAAGCCCAGTTTATCTG
2002 GCC
1 GCC
2005 CTAAAAGAAG
Statistics
Matches: 669, Mismatches: 93, Indels: 59
0.81 0.11 0.07
Matches are distributed among these distances:
31 11 0.02
32 123 0.18
33 489 0.73
34 46 0.07
ACGTcount: A:0.30, C:0.21, G:0.15, T:0.34
Consensus pattern (33 bp):
GCCATCAATGAAGCTTTAAGCCCAGTTTATCTG
Found at i:1254 original size:86 final size:86
Alignment explanation
Indices: 1096--1269 Score: 278
Period size: 86 Copynumber: 2.0 Consensus size: 86
1086 GTTTATCTGA
1096 CCATCAATGAAGCATTTAAGCCCAGTTTATCTGGCCATAAATGAAGCTTTAAGCCCAGTTTATCT
1 CCATCAATGAAGCATTTAAGCCCAGTTTATCTGGCCATAAATGAAGCTTTAAGCCCAGTTTATCT
1161 GGCCATCAATAAAATTTTAAG
66 GGCCATCAATAAAATTTTAAG
* * *
1182 CCATTAATGAAG-TTTTAAGCCCAGTTTATCTGGCCATCAATGAAGCATTTAAGCCCAGTTTATC
1 CCATCAATGAAGCATTTAAGCCCAGTTTATCTGGCCATAAATGAAGC-TTTAAGCCCAGTTTATC
* * *
1246 TGGTCATCAATGAAGTTTTAAG
65 TGGCCATCAATAAAATTTTAAG
1268 CC
1 CC
1270 TAGTTTATCT
Statistics
Matches: 81, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
85 32 0.40
86 49 0.60
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.32
Consensus pattern (86 bp):
CCATCAATGAAGCATTTAAGCCCAGTTTATCTGGCCATAAATGAAGCTTTAAGCCCAGTTTATCT
GGCCATCAATAAAATTTTAAG
Found at i:1275 original size:119 final size:119
Alignment explanation
Indices: 1062--1302 Score: 394
Period size: 119 Copynumber: 2.0 Consensus size: 119
1052 AGTTTATCTG
*
1062 GCCATTAATGAAGTTTTAAGTCCAGTTTATCTGACCATCAATGAAGCATTTAAGCCCAGTTTATC
1 GCCATTAATGAAGTTTTAAGCCCAGTTTATCTGACCATCAATGAAGCATTTAAGCCCAGTTTATC
*
1127 TGGCCATAAATGAAGCTTTAAGCCCAGTTTATCTGGC-CATCAATAAAATTTTAA
66 TGGCCATAAATGAAGCTTTAAGCCCAGTTTATCTAGCTC-TCAATAAAATTTTAA
*
1181 GCCATTAATGAAGTTTTAAGCCCAGTTTATCTGGCCATCAATGAAGCATTTAAGCCCAGTTTATC
1 GCCATTAATGAAGTTTTAAGCCCAGTTTATCTGACCATCAATGAAGCATTTAAGCCCAGTTTATC
* * * * *
1246 TGGTCATCAATGAAGTTTTAAGCCTAGTTTATCTAGCTCTCAATGAAATTTTAA
66 TGGCCATAAATGAAGCTTTAAGCCCAGTTTATCTAGCTCTCAATAAAATTTTAA
1300 GCC
1 GCC
1303 CAATTTATCT
Statistics
Matches: 113, Mismatches: 8, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
119 112 0.99
120 1 0.01
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.34
Consensus pattern (119 bp):
GCCATTAATGAAGTTTTAAGCCCAGTTTATCTGACCATCAATGAAGCATTTAAGCCCAGTTTATC
TGGCCATAAATGAAGCTTTAAGCCCAGTTTATCTAGCTCTCAATAAAATTTTAA
Found at i:2721 original size:22 final size:22
Alignment explanation
Indices: 2693--2757 Score: 85
Period size: 23 Copynumber: 2.9 Consensus size: 22
2683 TTTTAAGATT
2693 TGTAAGACCTCCGGGCATAATC
1 TGTAAGACCTCCGGGCATAATC
* * *
2715 TGTAAGACCTTCGAGCATGATTC
1 TGTAAGACCTCCGGGCAT-AATC
*
2738 TATAAGACCTCCGGGCATAA
1 TGTAAGACCTCCGGGCATAA
2758 ATTTGATTCA
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
22 17 0.49
23 18 0.51
ACGTcount: A:0.29, C:0.25, G:0.22, T:0.25
Consensus pattern (22 bp):
TGTAAGACCTCCGGGCATAATC
Found at i:2900 original size:22 final size:23
Alignment explanation
Indices: 2863--2906 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
2853 ACCTCCAAAC
*
2863 ATGATTTTGTAAGACCTCTGGGT
1 ATGATTTTCTAAGACCTCTGGGT
*
2886 ATGA-TTTCTAAGACCTTTGGG
1 ATGATTTTCTAAGACCTCTGGG
2907 CATAAATTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.23, C:0.14, G:0.25, T:0.39
Consensus pattern (23 bp):
ATGATTTTCTAAGACCTCTGGGT
Found at i:3031 original size:176 final size:177
Alignment explanation
Indices: 2822--3369 Score: 672
Period size: 179 Copynumber: 3.1 Consensus size: 177
2812 ATCCCAGTAA
* * *
2822 ATTCTGTAAGACCTCCGGGTAATTCTGTAAGACCTCCAAACATGATTTTGTAAGACC-TCTGGGT
1 ATTCTATAAGACCTCCGGGTAATTCTGTAAGACCTCCAGACATGATTTTGTAAGACCTTC-GGGC
* *
2886 ATGATTTCTAAGACCTTTGGGCATAAATTTGATTCGCAGTGTTATCTCGATCAATTCTTTATCTT
65 ATGATTTCTAAGACCTTCGGGCATAAATTTGATTCGCAGTGTTATCCCGATCAATTCTTTATCTT
*** * * * *
2951 TTGACTTACAATGTTATCCCAATCAATTCTGTAAGACCTTC-GGGCATG
130 TTGACTTATGGTGTTATCCCAATCGATTCTATAAGATC-TCAGGACATG
* * * * *
2999 ATT-TTTAAGACCTCCGGGTAATTCTATAAGACCTCCGGTCATGATTTTGTAAGACCTTCGAGCA
1 ATTCTATAAGACCTCCGGGTAATTCTGTAAGACCTCCAGACATGATTTTGTAAGACCTTCGGGCA
* * * *
3063 TGATTTCTAAGACCTCCGAGCATAAATTTGATTTGCTGTGTTATCCCGATCAATTCTTTATCTTT
66 TGATTTCTAAGACCTTCGGGCATAAATTTGATTCGCAGTGTTATCCCGATCAATTCTTTATCTTT
* ** *
3128 TGACTTGTGGTGTTATCTTAGTCGATTCTATAAGATCTCAGGACATG
131 TGACTTATGGTGTTATCCCAATCGATTCTATAAGATCTCAGGACATG
* ** * * * *
3175 ATTCTGTAAGACCTCCAGACATGATTCTGTAAGACCTCCAGACATGATTCTGTAAGACCTTCAGA
1 ATTCTATAAGACCTCC-G-GGTAATTCTGTAAGACCTCCAGACATGATTTTGTAAGACCTTCGGG
* ** *
3240 CATGATTTCTAAGA-CTTCCGGACATAAATTCAATTCGCGGTGTTATCCCGATCAATTCTTTATC
64 CATGATTTCTAAGACCTT-CGGGCATAAATTTGATTCGCAGTGTTATCCCGATCAATTCTTTATC
* * *
3304 TTTTAACTTATGGTGTTATCCCAATTGATTCTATAAGATCTCTGGACATG
128 TTTTGACTTATGGTGTTATCCCAATCGATTCTATAAGATCTCAGGACATG
3354 ATTCTATAAGACCTCC
1 ATTCTATAAGACCTCC
3370 AGACATAATT
Statistics
Matches: 315, Mismatches: 50, Indels: 10
0.84 0.13 0.03
Matches are distributed among these distances:
175 2 0.01
176 146 0.46
177 16 0.05
178 3 0.01
179 148 0.47
ACGTcount: A:0.26, C:0.21, G:0.17, T:0.36
Consensus pattern (177 bp):
ATTCTATAAGACCTCCGGGTAATTCTGTAAGACCTCCAGACATGATTTTGTAAGACCTTCGGGCA
TGATTTCTAAGACCTTCGGGCATAAATTTGATTCGCAGTGTTATCCCGATCAATTCTTTATCTTT
TGACTTATGGTGTTATCCCAATCGATTCTATAAGATCTCAGGACATG
Found at i:3052 original size:154 final size:152
Alignment explanation
Indices: 2689--3063 Score: 407
Period size: 154 Copynumber: 2.4 Consensus size: 152
2679 AAGATTTTAA
* * *
2689 GATTTGTAAGACCTCCGGGCATAA-TCTGTAAGACCTTCGAG-CATGATTCTATAAGACCTCCGG
1 GATTTGTAAGACCTCCGGG--TAATTCTGTAAGACCTCCG-GTCATGATTTTATAAGACCTTCGG
* * * **
2752 GCATAAATTTGATTCACGGTGTTATCCCGATCAATTTTTTATCTTTTGACTTGCGGTGTTATCCC
63 GCATAAATTTGATTCACAGTGTTATCCCGATCAATTCTTTATCTTTTGACTTACAATGTTATCCC
*
2817 AGTAAATTCTGTAAGACCTCCGGGT
128 AATAAATTCTGTAAGACCTCCGGGT
* *** * * * * *
2842 AATTCTGTAAGACCTCCAAACATGATTTTGTAAGACCTCTGGGT-ATGA-TTTCTAAGACCTTTG
1 GATT-TGTAAGACCTCC--GGGTAATTCTGTAAGACCTC-CGGTCATGATTTTATAAGACCTTCG
* *
2905 GGCATAAATTTGATTCGCAGTGTTATCTCGATCAATTCTTTATCTTTTGACTTACAATGTTATCC
62 GGCATAAATTTGATTCACAGTGTTATCCCGATCAATTCTTTATCTTTTGACTTACAATGTTATCC
* *
2970 CAATCAATTCTGTAAGACCTTCGGGCAT
127 CAATAAATTCTGTAAGACCTCCGGG--T
* * * *
2998 GATTTTTAAGACCTCCGGGTAATTCTATAAGACCTCCGGTCATGATTTTGTAAGACCTTCGAGCA
1 GATTTGTAAGACCTCCGGGTAATTCTGTAAGACCTCCGGTCATGATTTTATAAGACCTTCGGGCA
3063 T
66 T
3064 GATTTCTAAG
Statistics
Matches: 178, Mismatches: 34, Indels: 19
0.77 0.15 0.08
Matches are distributed among these distances:
152 3 0.02
153 21 0.12
154 122 0.69
155 27 0.15
156 5 0.03
ACGTcount: A:0.26, C:0.21, G:0.18, T:0.35
Consensus pattern (152 bp):
GATTTGTAAGACCTCCGGGTAATTCTGTAAGACCTCCGGTCATGATTTTATAAGACCTTCGGGCA
TAAATTTGATTCACAGTGTTATCCCGATCAATTCTTTATCTTTTGACTTACAATGTTATCCCAAT
AAATTCTGTAAGACCTCCGGGT
Found at i:3082 original size:22 final size:21
Alignment explanation
Indices: 2982--3085 Score: 84
Period size: 22 Copynumber: 4.7 Consensus size: 21
2972 ATCAATTCTG
* *
2982 TAAGACCTTCGGGCATGATTTT
1 TAAGACC-TCCGGCATGATTTA
* *
3004 TAAGACCTCCGG-GTAATTCTA
1 TAAGACCTCCGGCATGATT-TA
*
3025 TAAGACCTCCGGTCATGATTTTG
1 TAAGACCTCCGG-CATGA-TTTA
* *
3048 TAAGACCTTCGAGCATGATTTC
1 TAAGACCTCCG-GCATGATTTA
3070 TAAGACCTCCGAGCAT
1 TAAGACCTCCG-GCAT
3086 AAATTTGATT
Statistics
Matches: 67, Mismatches: 10, Indels: 10
0.77 0.11 0.11
Matches are distributed among these distances:
20 4 0.06
21 17 0.25
22 25 0.37
23 18 0.27
24 3 0.04
ACGTcount: A:0.26, C:0.23, G:0.20, T:0.31
Consensus pattern (21 bp):
TAAGACCTCCGGCATGATTTA
Found at i:3177 original size:23 final size:23
Alignment explanation
Indices: 3151--3264 Score: 151
Period size: 23 Copynumber: 5.0 Consensus size: 23
3141 TATCTTAGTC
* *
3151 GATTCTATAAGATCT-CAGGACAT
1 GATTCTGTAAGACCTCCA-GACAT
3174 GATTCTGTAAGACCTCCAGACAT
1 GATTCTGTAAGACCTCCAGACAT
3197 GATTCTGTAAGACCTCCAGACAT
1 GATTCTGTAAGACCTCCAGACAT
*
3220 GATTCTGTAAGACCTTCAGACAT
1 GATTCTGTAAGACCTCCAGACAT
* * *
3243 GATT-TCTAAGACTTCCGGACAT
1 GATTCTGTAAGACCTCCAGACAT
3265 AAATTCAATT
Statistics
Matches: 83, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
22 14 0.17
23 67 0.81
24 2 0.02
ACGTcount: A:0.31, C:0.23, G:0.18, T:0.29
Consensus pattern (23 bp):
GATTCTGTAAGACCTCCAGACAT
Found at i:3374 original size:23 final size:23
Alignment explanation
Indices: 3329--3375 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
3319 TTATCCCAAT
* **
3329 TGATTCTATAAGATCTCTGGACA
1 TGATTCTATAAGACCTCCAGACA
3352 TGATTCTATAAGACCTCCAGACA
1 TGATTCTATAAGACCTCCAGACA
3375 T
1 T
3376 AATTTCTAAG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.32, C:0.21, G:0.15, T:0.32
Consensus pattern (23 bp):
TGATTCTATAAGACCTCCAGACA
Found at i:3492 original size:133 final size:133
Alignment explanation
Indices: 3198--3484 Score: 330
Period size: 133 Copynumber: 2.2 Consensus size: 133
3188 TCCAGACATG
* * * *
3198 ATTCTGTAAGACCTCC-AGACATGATTCTGTAAGACCTTCAGACATGATTTCTAAGACTTCCGGA
1 ATTCTGTAAGACCTCCGA-ACATGATTCTATAAGACCTCCAGACATAATTTCTAAGACTTCAGGA
* * *
3262 CATAAATTCAATTCGCGGTGTTATCCCGATCAATTCTTTATCTTTTAACTTATGGTGTTATCCCA
65 CATAAATTCAATTCACGGTGTTATCCCGATCAATTCTTTATCTTCTAACTTATAGTGTTATCCCA
**
3327 ATTG
130 ATCA
* * * *
3331 ATTCTATAAGATCTCTGGACATGATTCTATAAGACCTCCAGACATAATTTCTAAGACTTTCAGG-
1 ATTCTGTAAGACCTCCGAACATGATTCTATAAGACCTCCAGACATAATTTCTAAGAC-TTCAGGA
** * * ** * *
3395 CATAAATTTGATTCATGGTGTTATCCTGATTGATTCTTTAT-TTCTGACTTGTAGTGTTAT-CCA
65 CATAAATTCAATTCACGGTGTTATCCCGATCAATTCTTTATCTTCTAACTTATAGTGTTATCCCA
3458 AGTCA
130 A-TCA
3463 ATTCTGTAAGACCTCCGAACAT
1 ATTCTGTAAGACCTCCGAACAT
3485 AATTTCTAAG
Statistics
Matches: 126, Mismatches: 25, Indels: 7
0.80 0.16 0.04
Matches are distributed among these distances:
131 4 0.03
132 34 0.27
133 83 0.66
134 5 0.04
ACGTcount: A:0.28, C:0.20, G:0.15, T:0.37
Consensus pattern (133 bp):
ATTCTGTAAGACCTCCGAACATGATTCTATAAGACCTCCAGACATAATTTCTAAGACTTCAGGAC
ATAAATTCAATTCACGGTGTTATCCCGATCAATTCTTTATCTTCTAACTTATAGTGTTATCCCAA
TCA
Found at i:3494 original size:22 final size:21
Alignment explanation
Indices: 3469--3541 Score: 67
Period size: 22 Copynumber: 3.4 Consensus size: 21
3459 GTCAATTCTG
3469 TAAGACCTCCGAACATAATTTC
1 TAAGACCTCCG-ACATAATTTC
* * *
3491 TAAGACTTCCGAC-CAATTCTG
1 TAAGACCTCCGACATAATT-TC
* *
3512 TAAGACCTCCGGACATGATTTT
1 TAAGACCTCC-GACATAATTTC
3534 TAAGACCT
1 TAAGACCT
3542 TCGGGCATAA
Statistics
Matches: 41, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
20 4 0.10
21 12 0.29
22 22 0.54
23 3 0.07
ACGTcount: A:0.32, C:0.26, G:0.14, T:0.29
Consensus pattern (21 bp):
TAAGACCTCCGACATAATTTC
Found at i:3517 original size:21 final size:23
Alignment explanation
Indices: 3461--3522 Score: 76
Period size: 21 Copynumber: 2.8 Consensus size: 23
3451 TTATCCAAGT
3461 CAATTCTGTAAGACCTCCGAACA
1 CAATTCTGTAAGACCTCCGAACA
* * *
3484 TAATT-TCTAAGACTTCCG-AC-
1 CAATTCTGTAAGACCTCCGAACA
3504 CAATTCTGTAAGACCTCCG
1 CAATTCTGTAAGACCTCCG
3523 GACATGATTT
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
20 4 0.12
21 13 0.41
22 11 0.34
23 4 0.12
ACGTcount: A:0.31, C:0.29, G:0.13, T:0.27
Consensus pattern (23 bp):
CAATTCTGTAAGACCTCCGAACA
Found at i:3631 original size:154 final size:152
Alignment explanation
Indices: 3354--3632 Score: 384
Period size: 152 Copynumber: 1.8 Consensus size: 152
3344 TCTGGACATG
* * *
3354 ATTCTATAAGACCTCCAGACATAATTTCTAAGACTTTCAGGCATAAATTTGATTCATGGTGTTAT
1 ATTCTATAAGACCTCCAGACATAATTTCTAAGACCTTCAGGCATAAATTCGATTCACGGTGTTAT
* *
3419 CCTGATTGATTCTTTATTTCTGACTTGTAGTGTTATCCAAGTCAATTCTGTAAGACCTCCGAACA
66 CCCGATCGATTCTTTATTTCTGACTTGTAGTGTTATCCAAGTCAATTCTGTAAGACCTCCGAACA
3484 TAATTTCTAAGACTTCCGACCA
131 TAATTTCTAAGACTTCCGACCA
* * * * *
3506 ATTCTGTAAGACCTCCGGACATGATTTTTAAGACCTTCGGGCATAAAATTCGATTCACGGTGTTA
1 ATTCTATAAGACCTCCAGACATAATTTCTAAGACCTTCAGGCAT-AAATTCGATTCACGGTGTTA
* *
3571 TCCCGATCGATTCTTTATCTTTTGAC-T-TACGATGTTATCCCAA-TCGATTCTGTAAGACCTCC
65 TCCCGATCGATTCTTTAT-TTCTGACTTGTA-G-TGTTAT-CCAAGTCAATTCTGTAAGACCTCC
3633 AGGCATGATT
Statistics
Matches: 110, Mismatches: 12, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
152 40 0.36
153 36 0.33
154 30 0.27
155 4 0.04
ACGTcount: A:0.27, C:0.22, G:0.15, T:0.36
Consensus pattern (152 bp):
ATTCTATAAGACCTCCAGACATAATTTCTAAGACCTTCAGGCATAAATTCGATTCACGGTGTTAT
CCCGATCGATTCTTTATTTCTGACTTGTAGTGTTATCCAAGTCAATTCTGTAAGACCTCCGAACA
TAATTTCTAAGACTTCCGACCA
Found at i:3646 original size:23 final size:23
Alignment explanation
Indices: 3616--3683 Score: 102
Period size: 23 Copynumber: 3.0 Consensus size: 23
3606 TATCCCAATC
*
3616 GATTCTGTAAGACCTCCAGGCAT
1 GATTCTGTAAGACCTCCGGGCAT
*
3639 GATTCTGTAAGACCTCCGGGTAT
1 GATTCTGTAAGACCTCCGGGCAT
*
3662 GATT-TCTAAGACCTCCGGGCAT
1 GATTCTGTAAGACCTCCGGGCAT
3684 AAATTCGATT
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
22 16 0.39
23 25 0.61
ACGTcount: A:0.24, C:0.25, G:0.24, T:0.28
Consensus pattern (23 bp):
GATTCTGTAAGACCTCCGGGCAT
Found at i:3747 original size:133 final size:134
Alignment explanation
Indices: 3506--3782 Score: 409
Period size: 133 Copynumber: 2.1 Consensus size: 134
3496 CTTCCGACCA
* *
3506 ATTCTGTAAGACCTCCGGACATGATTTTTAAGACCTTCGGGCATAAAATTCGATTCACGGTGTTA
1 ATTCTGTAAGACCTCCGGACATGATTTCTAAGACCTCCGGGCATAAAATTCGATTCACGGTGTTA
* *
3571 TCCCGATCGATTCTTTATCTTTTGACTTACGATGTTATCCCAATCGATTCTGTAAGACCTCCAGG
66 TCCCGATCGATTCTTTATCTTTTAACTTACGATGTTATCCCAATCGACTCTGTAAGACCTCCAGG
3636 CATG
131 CATG
** *
3640 ATTCTGTAAGACCTCCGGGTATGATTTCTAAGACCTCCGGGCAT-AAATTCGATTCGCGGTGTTA
1 ATTCTGTAAGACCTCCGGACATGATTTCTAAGACCTCCGGGCATAAAATTCGATTCACGGTGTTA
* * *
3704 TCCCGATTGATTCTTTAT-TTTTCAACTTAC-AGTGTTATTCCAATCGACTCTGTAAGACCTCCG
66 TCCCGATCGATTCTTTATCTTTT-AACTTACGA-TGTTATCCCAATCGACTCTGTAAGACCTCCA
*
3767 GGTATG
129 GGCATG
3773 ATT-TGTAAGA
1 ATTCTGTAAGA
3783 TCTTCGAACA
Statistics
Matches: 130, Mismatches: 11, Indels: 6
0.88 0.07 0.04
Matches are distributed among these distances:
132 12 0.09
133 78 0.60
134 40 0.31
ACGTcount: A:0.24, C:0.22, G:0.19, T:0.35
Consensus pattern (134 bp):
ATTCTGTAAGACCTCCGGACATGATTTCTAAGACCTCCGGGCATAAAATTCGATTCACGGTGTTA
TCCCGATCGATTCTTTATCTTTTAACTTACGATGTTATCCCAATCGACTCTGTAAGACCTCCAGG
CATG
Found at i:3835 original size:110 final size:110
Alignment explanation
Indices: 3642--3843 Score: 314
Period size: 110 Copynumber: 1.8 Consensus size: 110
3632 CAGGCATGAT
** * *
3642 TCTGTAAGACCTCCGGGTATGATTTCTAAGACCTCCGGGCATAAATTCGATTCGCGGTGTTATCC
1 TCTGTAAGACCTCCGGGTATGATTTCTAAGACCTCCGAACATAAATTCGATTCGCGATATTATCC
*
3707 CGATTGATTCTTTATTTTTCAACTTACAGTGTTATTCCAATCGAC
66 CGATTGATTCATTATTTTTCAACTTACAGTGTTATTCCAATCGAC
* * * * *
3752 TCTGTAAGACCTCCGGGTATGATTTGTAAGATCTTCGAACATAAATTCGATTTGCGATATTATCT
1 TCTGTAAGACCTCCGGGTATGATTTCTAAGACCTCCGAACATAAATTCGATTCGCGATATTATCC
3817 CGATTGATTCATTATTTTTCAACTTAC
66 CGATTGATTCATTATTTTTCAACTTAC
3844 GGTATCATCC
Statistics
Matches: 82, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
110 82 1.00
ACGTcount: A:0.25, C:0.20, G:0.17, T:0.38
Consensus pattern (110 bp):
TCTGTAAGACCTCCGGGTATGATTTCTAAGACCTCCGAACATAAATTCGATTCGCGATATTATCC
CGATTGATTCATTATTTTTCAACTTACAGTGTTATTCCAATCGAC
Found at i:4305 original size:20 final size:23
Alignment explanation
Indices: 4254--4298 Score: 72
Period size: 24 Copynumber: 1.9 Consensus size: 23
4244 TTCCAGCCAT
*
4254 AATCCCTTTCAATCTCTCTCTAGG
1 AATCCCCTTCAATCTCTCTCTA-G
4278 AATCCCCTTCAATCTCTCTCT
1 AATCCCCTTCAATCTCTCTCT
4299 GACCCCTATC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.20, C:0.38, G:0.04, T:0.38
Consensus pattern (23 bp):
AATCCCCTTCAATCTCTCTCTAG
Found at i:5597 original size:16 final size:16
Alignment explanation
Indices: 5566--5764 Score: 124
Period size: 16 Copynumber: 12.5 Consensus size: 16
5556 CTAAGTTTTT
5566 AAAACCCCTAAAAATCC
1 AAAACCCCT-AAAATCC
*
5583 AAAATCCCTAAAATCC
1 AAAACCCCTAAAATCC
* *
5599 AAACCCCCTAAAAATCT
1 AAAACCCCT-AAAATCC
* * *
5616 AAAATCCCTTAAATCT
1 AAAACCCCTAAAATCC
*
5632 AAACCCCCCTTAAAATCC
1 AAA-ACCCC-TAAAATCC
*
5650 GAAACCCCTAAAATCC
1 AAAACCCCTAAAATCC
*
5666 AAAACCCCCCAAAATCC
1 AAAA-CCCCTAAAATCC
* * **
5683 AAAATCCC-AAACTTT
1 AAAACCCCTAAAATCC
* * *
5698 TAAA-CTCTTAAA-CC
1 AAAACCCCTAAAATCC
*
5712 TAAACCCCCT-AAATCC
1 -AAAACCCCTAAAATCC
*
5728 AAAATCCCTAAAATCC
1 AAAACCCCTAAAATCC
*
5744 -AAA-CCCTTAAAT-C
1 AAAACCCCTAAAATCC
5757 AAAACCCC
1 AAAACCCC
5765 AAACCTCAAA
Statistics
Matches: 140, Mismatches: 31, Indels: 24
0.72 0.16 0.12
Matches are distributed among these distances:
13 1 0.01
14 13 0.09
15 27 0.19
16 48 0.34
17 43 0.31
18 8 0.06
ACGTcount: A:0.46, C:0.36, G:0.01, T:0.18
Consensus pattern (16 bp):
AAAACCCCTAAAATCC
Found at i:5607 original size:33 final size:33
Alignment explanation
Indices: 5570--5690 Score: 154
Period size: 33 Copynumber: 3.6 Consensus size: 33
5560 GTTTTTAAAA
5570 CCCCTAAAAATCCAAAATCCCTAAAATCCAAAC
1 CCCCTAAAAATCCAAAATCCCTAAAATCCAAAC
* * *
5603 CCCCTAAAAATCTAAAATCCCTTAAATCTAAACC
1 CCCCTAAAAATCCAAAATCCCTAAAATCCAAA-C
* * *
5637 CCCCTTAAAATCCGAAACCCCTAAAATCCAAAAC
1 CCCCTAAAAATCCAAAATCCCTAAAATCC-AAAC
*
5671 CCCC-CAAAATCCAAAATCCC
1 CCCCTAAAAATCCAAAATCCC
5691 AAACTTTTAA
Statistics
Matches: 74, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
33 42 0.57
34 29 0.39
35 3 0.04
ACGTcount: A:0.45, C:0.38, G:0.01, T:0.17
Consensus pattern (33 bp):
CCCCTAAAAATCCAAAATCCCTAAAATCCAAAC
Found at i:7329 original size:2 final size:2
Alignment explanation
Indices: 7317--7359 Score: 61
Period size: 2 Copynumber: 22.0 Consensus size: 2
7307 GGTCCATCCC
* *
7317 AT AT A- AT AT AT AT AT AT AT AT AT AT TT AT AC 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
7358 AT
1 AT
7360 TTTATAGCAT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:7492 original size:30 final size:30
Alignment explanation
Indices: 7456--7516 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
7446 ATGATTGAAA
7456 GTAAAAAATAATTCATATAATTATCCATTT
1 GTAAAAAATAATTCATATAATTATCCATTT
*
7486 GTAAAAAATAATTCATATAATTATCTATTT
1 GTAAAAAATAATTCATATAATTATCCATTT
7516 G
1 G
7517 CAACATCAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.46, C:0.08, G:0.05, T:0.41
Consensus pattern (30 bp):
GTAAAAAATAATTCATATAATTATCCATTT
Found at i:11646 original size:12 final size:12
Alignment explanation
Indices: 11629--11681 Score: 72
Period size: 12 Copynumber: 4.3 Consensus size: 12
11619 AAAATTATTT
11629 TTTAATTTTATA
1 TTTAATTTTATA
11641 TTTAATTTTATA
1 TTTAATTTTATA
*
11653 TTT-TTTATATATA
1 TTTAATT-T-TATA
11666 TTTAATTTTATA
1 TTTAATTTTATA
11678 TTTA
1 TTTA
11682 TATTAAAAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
11 2 0.06
12 24 0.67
13 8 0.22
14 2 0.06
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
TTTAATTTTATA
Found at i:11651 original size:25 final size:25
Alignment explanation
Indices: 11623--11680 Score: 82
Period size: 25 Copynumber: 2.3 Consensus size: 25
11613 ATATAAAAAA
*
11623 TTAT-TTTTTAATTTTATATTTAATT
1 TTATATTTTTAA-TATATATTTAATT
*
11648 TTATATTTTTTATATATATTTAATT
1 TTATATTTTTAATATATATTTAATT
11673 TTATATTT
1 TTATATTT
11681 ATATTAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
25 24 0.80
26 6 0.20
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (25 bp):
TTATATTTTTAATATATATTTAATT
Found at i:12264 original size:29 final size:29
Alignment explanation
Indices: 12210--12265 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
12200 TTTATTTTAA
* *
12210 AATAAAATATTCAAAACTTGATTAATTGT
1 AATAAAATATTCAAAACTTAAATAATTGT
12239 AATAAAATATT-ATAAACTTAAATAATT
1 AATAAAATATTCA-AAACTTAAATAATT
12266 ATTAAAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 1 0.04
29 23 0.96
ACGTcount: A:0.54, C:0.05, G:0.04, T:0.38
Consensus pattern (29 bp):
AATAAAATATTCAAAACTTAAATAATTGT
Found at i:12844 original size:2 final size:2
Alignment explanation
Indices: 12837--12865 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
12827 AACATTGCTC
12837 AT AT 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 AT AT A
12866 AAACATGTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:17402 original size:13 final size:13
Alignment explanation
Indices: 17386--17437 Score: 52
Period size: 13 Copynumber: 3.8 Consensus size: 13
17376 ATTAATCAAT
17386 TTATTTAAAAAAA
1 TTATTTAAAAAAA
**
17399 TTATTTAAATTAA
1 TTATTTAAAAAAA
17412 -TATTTAAACAAAAAA
1 TTATTT--A-AAAAAA
17427 TTATTTAAAAA
1 TTATTTAAAAA
17438 TTAAATATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
12 5 0.16
13 15 0.48
14 2 0.06
15 4 0.13
16 5 0.16
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (13 bp):
TTATTTAAAAAAA
Found at i:21876 original size:48 final size:49
Alignment explanation
Indices: 21824--21940 Score: 123
Period size: 50 Copynumber: 2.4 Consensus size: 49
21814 AACAAAATAC
* *
21824 TTTTAATAAAAGTAATTCTCACTTTACATA-TAAACAAACAAAAGTATTT
1 TTTTAATAAAAATAATTCTCACTTTACAGATTAAACAAACAAAA-TATTT
* * * * *
21873 TTTATAAAAAAAATAATTCCCACTTTATAGATTTAACAAATAAAATA-TT
1 TTT-TAATAAAAATAATTCTCACTTTACAGATTAAACAAACAAAATATTT
21922 TTTT-ATAAAAAATAATTCT
1 TTTTAAT-AAAAATAATTCT
21941 TGAAACAAAA
Statistics
Matches: 56, Mismatches: 9, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
47 1 0.02
48 12 0.21
49 8 0.14
50 24 0.43
51 11 0.20
ACGTcount: A:0.49, C:0.10, G:0.03, T:0.38
Consensus pattern (49 bp):
TTTTAATAAAAATAATTCTCACTTTACAGATTAAACAAACAAAATATTT
Found at i:21897 original size:50 final size:50
Alignment explanation
Indices: 21831--21933 Score: 136
Period size: 50 Copynumber: 2.1 Consensus size: 50
21821 TACTTTTAAT
* * *
21831 AAAAGTAATTCTCACTTTACATA-TAAACAAACAAAAGTATTTTTTATAAA
1 AAAAATAATTCCCACTTTACAGATTAAACAAACAAAA-TATTTTTTATAAA
* * *
21881 AAAAATAATTCCCACTTTATAGATTTAACAAATAAAATATTTTTTATAAA
1 AAAAATAATTCCCACTTTACAGATTAAACAAACAAAATATTTTTTATAAA
21931 AAA
1 AAA
21934 TAATTCTTGA
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
50 35 0.76
51 11 0.24
ACGTcount: A:0.51, C:0.11, G:0.03, T:0.35
Consensus pattern (50 bp):
AAAAATAATTCCCACTTTACAGATTAAACAAACAAAATATTTTTTATAAA
Found at i:22429 original size:21 final size:21
Alignment explanation
Indices: 22405--22445 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
22395 CCTTTGATAA
*
22405 AATTTTAATAATTTTCAATAC
1 AATTTTAATAATATTCAATAC
22426 AATTTTAATAATATTCAATA
1 AATTTTAATAATATTCAATA
22446 TTAGTTTGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.46, C:0.07, G:0.00, T:0.46
Consensus pattern (21 bp):
AATTTTAATAATATTCAATAC
Found at i:22584 original size:20 final size:22
Alignment explanation
Indices: 22546--22595 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
22536 TAACATTTCT
22546 TATAATTTTGGCAATTTA-TGA
1 TATAATTTTGGCAATTTATTGA
* *
22567 TATATTTTTGGTAA-TTATTGA
1 TATAATTTTGGCAATTTATTGA
*
22588 TAAAATTT
1 TATAATTT
22596 GTATTATTAT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
20 3 0.12
21 21 0.88
ACGTcount: A:0.34, C:0.02, G:0.12, T:0.52
Consensus pattern (22 bp):
TATAATTTTGGCAATTTATTGA
Found at i:22731 original size:12 final size:13
Alignment explanation
Indices: 22701--22730 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
22691 CATTCAAATT
22701 TAAAATTTTTTAA
1 TAAAATTTTTTAA
*
22714 TAAAATTTTTTAT
1 TAAAATTTTTTAA
22727 TAAA
1 TAAA
22731 TAAGTTCATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (13 bp):
TAAAATTTTTTAA
Found at i:22905 original size:22 final size:21
Alignment explanation
Indices: 22880--22960 Score: 63
Period size: 22 Copynumber: 3.7 Consensus size: 21
22870 TCAATAATAT
22880 GTTATCAATGATTTATTATTAA
1 GTTAT-AATGATTTATTATTAA
* * *
22902 GTTAATGATTATTTATTATAAA
1 GTT-ATAATGATTTATTATTAA
* *
22924 GTTATAATTTATTTACTATTAA
1 GTTATAA-TGATTTATTATTAA
* *
22946 TTTATCGATGATTTA
1 GTTAT-AATGATTTA
22961 ATTCAAAATT
Statistics
Matches: 47, Mismatches: 9, Indels: 6
0.76 0.15 0.10
Matches are distributed among these distances:
21 3 0.06
22 41 0.87
23 3 0.06
ACGTcount: A:0.36, C:0.04, G:0.09, T:0.52
Consensus pattern (21 bp):
GTTATAATGATTTATTATTAA
Found at i:23005 original size:22 final size:22
Alignment explanation
Indices: 22980--23049 Score: 61
Period size: 22 Copynumber: 3.0 Consensus size: 22
22970 TATTAATGAT
22980 TAACTAATTTATTACTAAATTA
1 TAACTAATTTATTACTAAATTA
** *
23002 TAACCGATTTATGACTATTAAGTTA
1 TAACTAATTTATTACTA--AA-TTA
*
23027 TTAA-TAATTTACTACTAAATTA
1 -TAACTAATTTATTACTAAATTA
23049 T
1 T
23050 CAATAAATTA
Statistics
Matches: 37, Mismatches: 7, Indels: 9
0.70 0.13 0.17
Matches are distributed among these distances:
21 1 0.03
22 17 0.46
23 2 0.05
24 2 0.05
25 12 0.32
26 3 0.08
ACGTcount: A:0.41, C:0.10, G:0.04, T:0.44
Consensus pattern (22 bp):
TAACTAATTTATTACTAAATTA
Found at i:23054 original size:22 final size:22
Alignment explanation
Indices: 23015--23312 Score: 133
Period size: 22 Copynumber: 13.7 Consensus size: 22
23005 CCGATTTATG
* *
23015 ACTATTAAGTTATTAATAATTT
1 ACTATTAAATTATCAATAATTT
* *
23037 ACTACTAAATTATCAATAAATT
1 ACTATTAAATTATCAATAATTT
* ** *
23059 ACTAATATGTTAT-TATACATTT
1 ACTATTAAATTATCAATA-ATTT
* * *
23081 ACTATTATATTATCATTTATTT
1 ACTATTAAATTATCAATAATTT
* * * * *
23103 ACAATCT-AGTTTTCGATTATTT
1 ACTAT-TAAATTATCAATAATTT
* *
23125 ACTATAAAATCATC-ATATATTT
1 ACTATTAAATTATCAATA-ATTT
* *
23147 A-TATTAAATTATCTATAATTC
1 ACTATTAAATTATCAATAATTT
** * * *
23168 ACTACCAATTTATCATTGATTT
1 ACTATTAAATTATCAATAATTT
*
23190 AC-ATTAAAATTTTC-ATAATTT
1 ACTATT-AAATTATCAATAATTT
* * * * *
23211 ATTATTAAGTTATCATTGATTA
1 ACTATTAAATTATCAATAATTT
* *
23233 ACTATTAAGTTATCGATAATTT
1 ACTATTAAATTATCAATAATTT
** *
23255 ACTATTAGGTTAT-ATTAATTT
1 ACTATTAAATTATCAATAATTT
* * * * *
23276 ACTTTTAATTTTTCAATGATTA
1 ACTATTAAATTATCAATAATTT
*
23298 ACTACTAAATTATCA
1 ACTATTAAATTATCA
23313 CTTATCTATT
Statistics
Matches: 198, Mismatches: 67, Indels: 22
0.69 0.23 0.08
Matches are distributed among these distances:
21 47 0.24
22 149 0.75
23 2 0.01
ACGTcount: A:0.38, C:0.10, G:0.04, T:0.48
Consensus pattern (22 bp):
ACTATTAAATTATCAATAATTT
Found at i:23254 original size:44 final size:43
Alignment explanation
Indices: 23152--23267 Score: 117
Period size: 43 Copynumber: 2.7 Consensus size: 43
23142 TATTTATATT
* ** * *
23152 AAATTATCTATAATTCACTACCAATTTATCATTGATTTACATTA
1 AAATTATC-ATAATTTACTATTAAGTTATCATTGATTAACATTA
* *
23196 AAATTTTCATAATTTATTATTAAGTTATCATTGATTAACTATT-
1 AAATTATCATAATTTACTATTAAGTTATCATTGATTAAC-ATTA
* *
23239 AAGTTATCGATAATTTACTATTAGGTTAT
1 AAATTATC-ATAATTTACTATTAAGTTAT
23268 ATTAATTTAC
Statistics
Matches: 59, Mismatches: 11, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
43 31 0.53
44 28 0.47
ACGTcount: A:0.37, C:0.10, G:0.06, T:0.47
Consensus pattern (43 bp):
AAATTATCATAATTTACTATTAAGTTATCATTGATTAACATTA
Found at i:23326 original size:65 final size:64
Alignment explanation
Indices: 23205--23372 Score: 153
Period size: 65 Copynumber: 2.6 Consensus size: 64
23195 AAAATTTTCA
* * * * * *
23205 TAATTTA-TTATTAAGTTATCATTGATTAACTATTAAGTTATCGATAATTTACTATTAGGTTATA
1 TAATTTACTT-TTAATTTATCAATGATTAACTACTAAATTATCGATAATCTACTATTAAGTT-TA
23269 T
64 T
* * * *
23270 TAATTTACTTTTAATTTTTCAATGATTAACTACTAAATTATC-ACTTATCTATTATTAAGTTTTT
1 TAATTTACTTTTAATTTATCAATGATTAACTACTAAATTATCGA-TAATCTACTATTAAGTTTAT
* *
23334 TATTATTTACTATTAAGTTTATCAATGAATAA-TACTAAA
1 TA--ATTTACTTTTAA-TTTATCAATGATTAACTACTAAA
23373 CTGAAACTGA
Statistics
Matches: 85, Mismatches: 13, Indels: 9
0.79 0.12 0.08
Matches are distributed among these distances:
64 5 0.06
65 47 0.55
66 20 0.24
67 13 0.15
ACGTcount: A:0.36, C:0.08, G:0.06, T:0.49
Consensus pattern (64 bp):
TAATTTACTTTTAATTTATCAATGATTAACTACTAAATTATCGATAATCTACTATTAAGTTTAT
Found at i:23796 original size:22 final size:22
Alignment explanation
Indices: 23736--23963 Score: 106
Period size: 22 Copynumber: 10.5 Consensus size: 22
23726 ATGATAGACA
* * *
23736 ATTAAGTTATTATTAATTTGCT
1 ATTAAATTATTAATAATTTACT
** * *
23758 GCTATATTATTAGTAATTTACT
1 ATTAAATTATTAATAATTTACT
* *
23780 ATTAATTTTTTAATAATTTACT
1 ATTAAATTATTAATAATTTACT
* * * * *
23802 AATAAATTGTCAATGATTTATT
1 ATTAAATTATTAATAATTTACT
* * * *
23824 AGTAATTTATTAATGATTTACC
1 ATTAAATTATTAATAATTTACT
* * *
23846 ATTAAGTTATAAATAATTTACC
1 ATTAAATTATTAATAATTTACT
* *
23868 ATTAAATTGTTGAT-ATTTACT
1 ATTAAATTATTAATAATTTACT
* * * *
23889 ACTAAGTTATTGATAA-TTATT
1 ATTAAATTATTAATAATTTACT
*
23910 A-TAAAGTTA-TAATGGATTTACT
1 ATTAAA-TTATTAAT-AATTTACT
* * *
23932 A-TAAATTTATCAATGATTTATT
1 ATTAAA-TTATTAATAATTTACT
*
23954 ATAAAATTAT
1 ATTAAATTAT
23964 CATTGATTAA
Statistics
Matches: 155, Mismatches: 45, Indels: 12
0.73 0.21 0.06
Matches are distributed among these distances:
20 6 0.04
21 26 0.17
22 117 0.75
23 6 0.04
ACGTcount: A:0.39, C:0.06, G:0.07, T:0.48
Consensus pattern (22 bp):
ATTAAATTATTAATAATTTACT
Found at i:23833 original size:11 final size:11
Alignment explanation
Indices: 23764--23843 Score: 61
Period size: 11 Copynumber: 7.3 Consensus size: 11
23754 TGCTGCTATA
*
23764 TTATTAGTAAT
1 TTATTAATAAT
* *
23775 TTACTATTAAT
1 TTATTAATAAT
*
23786 TTTTTAATAAT
1 TTATTAATAAT
* *
23797 TTACTAATAAA
1 TTATTAATAAT
* * *
23808 TTGTCAATGAT
1 TTATTAATAAT
*
23819 TTATTAGTAAT
1 TTATTAATAAT
*
23830 TTATTAATGAT
1 TTATTAATAAT
23841 TTA
1 TTA
23844 CCATTAAGTT
Statistics
Matches: 50, Mismatches: 19, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
11 50 1.00
ACGTcount: A:0.38, C:0.04, G:0.06, T:0.53
Consensus pattern (11 bp):
TTATTAATAAT
Found at i:23964 original size:22 final size:22
Alignment explanation
Indices: 23905--23971 Score: 82
Period size: 22 Copynumber: 3.0 Consensus size: 22
23895 TTATTGATAA
*
23905 TTATTATAAAGTTAT-AATGGAT
1 TTATTATAAAATTATCAAT-GAT
* *
23927 TTACTATAAATTTATCAATGAT
1 TTATTATAAAATTATCAATGAT
*
23949 TTATTATAAAATTATCATTGAT
1 TTATTATAAAATTATCAATGAT
23971 T
1 T
23972 AACTAATTTA
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
22 36 0.92
23 3 0.08
ACGTcount: A:0.40, C:0.04, G:0.07, T:0.48
Consensus pattern (22 bp):
TTATTATAAAATTATCAATGAT
Found at i:24094 original size:22 final size:21
Alignment explanation
Indices: 24041--24115 Score: 89
Period size: 22 Copynumber: 3.5 Consensus size: 21
24031 ATTATTTGTG
* *
24041 ATTTAATATTAAGTTATCAAT
1 ATTTATTATTAAATTATCAAT
*
24062 -TTTGTTATTAAATTATCAAT
1 ATTTATTATTAAATTATCAAT
24082 AATTTATTATTAAATTATCAAT
1 -ATTTATTATTAAATTATCAAT
*
24104 GATTTACTATTA
1 -ATTTATTATTA
24116 TTTATTATGC
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
20 17 0.37
22 29 0.63
ACGTcount: A:0.40, C:0.05, G:0.04, T:0.51
Consensus pattern (21 bp):
ATTTATTATTAAATTATCAAT
Found at i:24334 original size:22 final size:23
Alignment explanation
Indices: 24291--24342 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 23
24281 TATATTTTTT
*
24291 AAAATTATTTAATAATTAACTAC
1 AAAATTATATAATAATTAACTAC
* *
24314 AAAATT-TATAATTATTTACTAC
1 AAAATTATATAATAATTAACTAC
24336 -AAATTAT
1 AAAATTAT
24343 CTTTGATTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
21 5 0.20
22 14 0.56
23 6 0.24
ACGTcount: A:0.50, C:0.08, G:0.00, T:0.42
Consensus pattern (23 bp):
AAAATTATATAATAATTAACTAC
Found at i:24757 original size:23 final size:23
Alignment explanation
Indices: 24727--24776 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
24717 GATATATTGC
24727 TATTA-TTTTTATTAATTTAAAAA
1 TATTATTTTTTATT-ATTTAAAAA
*
24750 TATTATTTTTTATTATTTAAAAC
1 TATTATTTTTTATTATTTAAAAA
24773 TATT
1 TATT
24777 TTTAACATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 17 0.68
24 8 0.32
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (23 bp):
TATTATTTTTTATTATTTAAAAA
Found at i:25955 original size:22 final size:23
Alignment explanation
Indices: 25929--25985 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 23
25919 TTATTGATTT
25929 ACTATTAAGTTATAAATT-ATTG
1 ACTATTAAGTTATAAATTCATTG
* ** *
25951 ACTATTAAATT-TTCATTCATTT
1 ACTATTAAGTTATAAATTCATTG
25973 ACTATTAAGTTAT
1 ACTATTAAGTTAT
25986 CACTAACTTA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
21 4 0.14
22 23 0.82
23 1 0.04
ACGTcount: A:0.37, C:0.09, G:0.05, T:0.49
Consensus pattern (23 bp):
ACTATTAAGTTATAAATTCATTG
Found at i:26822 original size:9 final size:10
Alignment explanation
Indices: 26797--26821 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
26787 AGAAATTTTC
26797 AAAAAATTCT
1 AAAAAATTCT
26807 AAAAAATTCT
1 AAAAAATTCT
26817 AAAAA
1 AAAAA
26822 TATATATAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.68, C:0.08, G:0.00, T:0.24
Consensus pattern (10 bp):
AAAAAATTCT
Found at i:26977 original size:31 final size:31
Alignment explanation
Indices: 26922--26997 Score: 113
Period size: 29 Copynumber: 2.5 Consensus size: 31
26912 ATGAAACTTT
26922 AAATTTTCAATAAAAAATTAATAAAAAATCCAA
1 AAATTTTCAATAAAAAATTAATAAAAAA--CAA
26955 AAATTTTCAA-AAAAAATT-ATAAAAAACAA
1 AAATTTTCAATAAAAAATTAATAAAAAACAA
26984 AAATTTT-AATAAAA
1 AAATTTTCAATAAAA
26998 TAAAGTATTC
Statistics
Matches: 42, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
28 2 0.05
29 14 0.33
31 8 0.19
32 8 0.19
33 10 0.24
ACGTcount: A:0.66, C:0.07, G:0.00, T:0.28
Consensus pattern (31 bp):
AAATTTTCAATAAAAAATTAATAAAAAACAA
Found at i:27201 original size:17 final size:17
Alignment explanation
Indices: 27181--27213 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
27171 TATTTTTAGT
27181 TTTTTAAAATTTTAAAA
1 TTTTTAAAATTTTAAAA
*
27198 TTTTTTAAATTTTAAA
1 TTTTTAAAATTTTAAA
27214 TAATTTTTTT
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:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TTTTTAAAATTTTAAAA
Found at i:27278 original size:27 final size:25
Alignment explanation
Indices: 27173--27343 Score: 78
Period size: 26 Copynumber: 6.4 Consensus size: 25
27163 AATTTTTTTA
* *
27173 TTTTTAGTTTTTTAAAATTTTAAAAT
1 TTTTTAGATTTTTAAAATTTT-TAAT
* * *
27199 TTTTTAAATTTTAAATAATTTTT-TT
1 TTTTTAGATTTTTAA-AATTTTTAAT
* * * *
27224 TTTATTAAAATTTT-CATTTTCTTGAAT
1 TTT-TTAGATTTTTAAAATTT-TT-AAT
27251 TTTTTAGATTTTTATCAAATTTTTAATT
1 TTTTTAGATTTTTA--AAATTTTTAA-T
* * *
27279 TTTTTTGAATTTTTAAAATTATTAAA
1 TTTTTAG-ATTTTTAAAATTTTTAAT
* *
27305 ATTTTATGATTTTTAAGAAATTTTCATAT
1 TTTTTA-GATTTTT-A-AAATTTTTA-AT
27334 TTTTTA-ATTT
1 TTTTTAGATTT
27344 GAAATTAGTT
Statistics
Matches: 108, Mismatches: 23, Indels: 27
0.68 0.15 0.17
Matches are distributed among these distances:
24 4 0.04
25 6 0.06
26 38 0.35
27 27 0.25
28 16 0.15
29 17 0.16
ACGTcount: A:0.32, C:0.02, G:0.04, T:0.62
Consensus pattern (25 bp):
TTTTTAGATTTTTAAAATTTTTAAT
Found at i:27289 original size:18 final size:18
Alignment explanation
Indices: 27222--27294 Score: 58
Period size: 18 Copynumber: 4.0 Consensus size: 18
27212 AATAATTTTT
* * *
27222 TTTTTATTAAAATTTTCA
1 TTTTTATTGAATTTTTAA
*
27240 -TTTTCTTGAATTTTTTAGA
1 TTTTTATTGAA-TTTTTA-A
**
27259 TTTTTATCAAATTTTTAA
1 TTTTTATTGAATTTTTAA
*
27277 TTTTTTTTGAATTTTTAA
1 TTTTTATTGAATTTTTAA
27295 AATTATTAAA
Statistics
Matches: 42, Mismatches: 10, Indels: 6
0.72 0.17 0.10
Matches are distributed among these distances:
17 8 0.19
18 20 0.48
19 7 0.17
20 7 0.17
ACGTcount: A:0.27, C:0.04, G:0.04, T:0.64
Consensus pattern (18 bp):
TTTTTATTGAATTTTTAA
Found at i:27317 original size:37 final size:36
Alignment explanation
Indices: 27225--27318 Score: 93
Period size: 38 Copynumber: 2.6 Consensus size: 36
27215 AATTTTTTTT
* * *
27225 TTATTAAAA-TTTTCA-TTTTCTTGAATTTTTTAGA
1 TTATTAAAATTTTTAATTTTTCTTGAATTTTTAAAA
* *
27259 TTTTTATCAAATTTTTAATTTTTTTTGAATTTTTAAAA
1 TTATTA--AAATTTTTAATTTTTCTTGAATTTTTAAAA
*
27297 TTATTAAAATTTTATGATTTTT
1 TTATTAAAATTTT-TAATTTTT
27319 AAGAAATTTT
Statistics
Matches: 48, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
34 5 0.10
36 10 0.21
37 12 0.25
38 21 0.44
ACGTcount: A:0.31, C:0.03, G:0.04, T:0.62
Consensus pattern (36 bp):
TTATTAAAATTTTTAATTTTTCTTGAATTTTTAAAA
Found at i:27337 original size:54 final size:52
Alignment explanation
Indices: 27252--27383 Score: 124
Period size: 54 Copynumber: 2.5 Consensus size: 52
27242 TTCTTGAATT
* * *
27252 TTTTA-GATTTTTATCAAATTTTTAATTTTTTTTGAATTTTTAAAATTA-TTAAAA
1 TTTTATGATTTTTA-AAAAATTTTAATATTTTTT-AA--TTTAAAATTAGTTAAAA
* * * *
27306 TTTTATGATTTTTAAGAAATTTTCATATTTTTTAATTTGAAATTAGTTATAA
1 TTTTATGATTTTTAAAAAATTTTAATATTTTTTAATTTAAAATTAGTTAAAA
*
27358 TTTTTTGTATTTTTTAAAAAATTTTA
1 TTTTATG-A-TTTTTAAAAAATTTTA
27384 TGAAATCTTC
Statistics
Matches: 64, Mismatches: 10, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
51 9 0.14
52 11 0.17
53 3 0.05
54 33 0.52
55 8 0.12
ACGTcount: A:0.34, C:0.02, G:0.05, T:0.59
Consensus pattern (52 bp):
TTTTATGATTTTTAAAAAATTTTAATATTTTTTAATTTAAAATTAGTTAAAA
Found at i:29240 original size:20 final size:20
Alignment explanation
Indices: 29215--29253 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
29205 CACATTTTAT
29215 ATATATAAACAAATAGATAG
1 ATATATAAACAAATAGATAG
* *
29235 ATATATAGATAAATAGATA
1 ATATATAAACAAATAGATA
29254 TATAAAAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.59, C:0.03, G:0.10, T:0.28
Consensus pattern (20 bp):
ATATATAAACAAATAGATAG
Done.