Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013049.1 Corchorus olitorius cultivar O-4 contig13082, 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: 9894
ACGTcount: A:0.30, C:0.20, G:0.16, T:0.34
Found at i:281 original size:154 final size:154
Alignment explanation
Indices: 1--832 Score: 1193
Period size: 154 Copynumber: 5.4 Consensus size: 154
* * *
1 CTAACTATATTCATTTTTGTGAGATTAGTCCACTTTGAAGTTTTTAGCTCATTTGGAACACTTGT
1 CTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGT
*
66 TATTCTGGGCCTATCGCGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAAG
66 TATTTTGGGCCTATCGCGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAAG
*
131 GCTTTTCTTTCCATTGTTTATGAC
131 GCTTTTCTTTCCATTGTTTATGGC
*
155 CTAACTATAATCATTTTGGTGAGATTAGTCCATTGTGAAGTTTTTAGCTCATTTGGAACACTTGT
1 CTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGT
** * *
220 TATTTTGGATCTATCGCAGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTTGCAAACCTCAAG
66 TATTTTGGGCCTATCGCGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAAG
285 GCTTTTCTTTCCATTGTTTATGGC
131 GCTTTTCTTTCCATTGTTTATGGC
* * * * * *
309 CTCACAAAAATCATTTTGGTGAGATTATTCTACTGTGAAGTATTTAGCTCATTTGGAACACTTG-
1 CTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGT
* ** * * *
373 TACTTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTTAATCGTCTTCAATTAGGCAAACCTCAA
66 TA-TTTTGGGCCTATCGCGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAA
* * *
438 AGCTATTCTTT-AAGTTGTTTATGGC
130 GGCTTTTCTTTCCA-TTGTTTATGGC
* *
463 CTAACTATAATCATTTTGATGAGATTAGTCCACTGTGAAGTTCTTAGCTCATTTGGAACACTTGT
1 CTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGT
* * *
528 TATTTTGGGCCTATCGCGGCCCATTAGTGACGTTTTGGATCGTCTTCGATTTGGCAAACTTCAAT
66 TATTTTGGGCCTATCGCGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAAG
593 GCTTTTCTTTCCATTGTTTATGGC
131 GCTTTTCTTTCCATTGTTTATGGC
* * *
617 CTTACTATAATCAATTTGGTGTAGATTAGTCCACTGTGAAGTTCTTAGCTCATTTGGAACACTTG
1 CTAACTATAATCATTTTGGTG-AGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTG
* * ** *
682 TTCTTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCGA
65 TTATTTTGGGCCTATCGCGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAA
* *
747 TGCTTTTCTTTCTATTGTTTATGGC
130 GGCTTTTCTTTCCATTGTTTATGGC
* * * **
772 CAAAACTATAATCATTATT-GTTAGATTACTCCACTGTGAAGCGTTTAGCTCATTTGGAACA
1 C-TAACTATAATCATT-TTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACA
833 ATTTGGGAAA
Statistics
Matches: 603, Mismatches: 68, Indels: 13
0.88 0.10 0.02
Matches are distributed among these distances:
153 3 0.00
154 421 0.70
155 164 0.27
156 13 0.02
157 2 0.00
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.40
Consensus pattern (154 bp):
CTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGT
TATTTTGGGCCTATCGCGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAAG
GCTTTTCTTTCCATTGTTTATGGC
Found at i:923 original size:104 final size:102
Alignment explanation
Indices: 731--936 Score: 247
Period size: 104 Copynumber: 2.0 Consensus size: 102
721 ATCGTCTTCG
* * *
731 ATTTGGCAAACCTCGATGCTTTTCTTTCTATTGTTTATGGCCAAAACTATAATCATTATTGTTAG
1 ATTTGGCAAACCTCGATGCTTTGCTTTCCATTGTTTATGGCCAAAACTATAATCATTATTGTGAG
* *
796 ATTACTCCACTGTGAAGCGTTTAGCTCATTTGGAACA
66 ATTACACCACTGTGAAGCGTTTAGATCATTTGGAACA
* **
833 ATTTGGGAAACCTCGAATTGC-TTGCTTTCCATTGTTTACTGG-CGTAACTATAATCATT-TTAG
1 ATTTGGCAAACCTCG-A-TGCTTTGCTTTCCATTGTTTA-TGGCCAAAACTATAATCATTATT--
* **
895 GTGAGATTAGACCACTGTGAAGTTTTTAGATCATTTGGAACA
61 GTGAGATTACACCACTGTGAAGCGTTTAGATCATTTGGAACA
937 CTTGTTATTT
Statistics
Matches: 88, Mismatches: 11, Indels: 8
0.82 0.10 0.07
Matches are distributed among these distances:
102 16 0.18
103 30 0.34
104 42 0.48
ACGTcount: A:0.27, C:0.17, G:0.18, T:0.38
Consensus pattern (102 bp):
ATTTGGCAAACCTCGATGCTTTGCTTTCCATTGTTTATGGCCAAAACTATAATCATTATTGTGAG
ATTACACCACTGTGAAGCGTTTAGATCATTTGGAACA
Found at i:1140 original size:153 final size:153
Alignment explanation
Indices: 833--3661 Score: 4126
Period size: 153 Copynumber: 18.5 Consensus size: 153
823 ATTTGGAACA
* *
833 ATTTGGGAAACCTCGAATTGC-TTGCTTTCCATTGTTTACTGGCGTAACTATAATCATTTTAGGT
1 ATTTGGGAAACCTC-AA-TGCTTTTCTTTCCATTGTTTA-TGGCCTAACTATAATCATTTT-GGT
* * *
897 GAGATTAGACCACTGTGAAGTTTTTAGATCATTTGGAACACTTGTTATTTTGGACCTATCGGGGC
62 GAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATC-GGGC
962 CCATTAGTTCCGTTTTGAATCGTCTTCG
126 CCATTAGTTCCGTTTTGAATCGTCTTCG
* *
990 ATTTGGGAAACCCCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTTGTGAGA
1 ATTTGGGAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGA
1055 TTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTG-TATTTTGGGCCTATCGGGGCCCAT
66 TTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATC-GGGCCCAT
1119 TAGTTCCGTTTTGAATCGTCTTCG
130 TAGTTCCGTTTTGAATCGTCTTCG
* * *
1143 ATTTGGGAAACATCAATGCTTTTCGTTCCATTGATTATGGCCTAACTATAATCATTTTGGTGAGA
1 ATTTGGGAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGA
* * *
1208 TTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTCTTATCTTGGGCCTATCGGGCCCACT
66 TTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGCCCATT
* *
1273 ACTTCCGTTTTGAATCATCTTCG
131 AGTTCCGTTTTGAATCGTCTTCG
* * * * * *
1296 ACTTGGCAACCCTCAATTCTTTGT-TTTCCATTGTTTATGGCCTAACTGTAATCATTATGGTGAG
1 ATTTGGGAAACCTCAATGCTTT-TCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAG
* * * *
1360 ATTAGTCCACTTTGAAGTTTTTAACTCATTTGGAACACTTGTTATTTTGGGCCAATCAGGCCCCA
65 ATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATC-GGGCCCA
** * *
1425 TTAGTGACATTTTGAATAGTCTTCG
129 TTAGTTCCGTTTTGAATCGTCTTCG
*
1450 ATTTGGGAAACCTCAATGCTTTTCTTT-CATTGATTATGGCCTAACTATAATCATTTTGGTGAGA
1 ATTTGGGAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGA
* *
1514 TTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTAGACCTATCGGGCCCATT
66 TTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGCCCATT
1579 AGTTCCGTTTTGAATCGTCTTCG
131 AGTTCCGTTTTGAATCGTCTTCG
** * * * *
1602 ACTTT--GCTACTCTCAATTCTTTTCTTTCCATTGTTTATGGCCTAACTGTAATCATTATCGTGA
1 A-TTTGGGAAAC-CTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGA
* *
1665 GATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGACCTATCAGGGCCT
64 GATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATC-GGGCCC
* *
1730 ATTAGATCTGTTTTGAATCGTCTTCG
128 ATTAGTTCCGTTTTGAATCGTCTTCG
* * * *
1756 ATTTGGCAACCCTCAATGTTTTTCTTTCCATTGTTTATGGCCTAAC-AGTAATCATTATGGTGAG
1 ATTTGGGAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTA-TAATCATTTTGGTGAG
* * * *
1820 ATTAGTCCACTTTGAAGATTTTAGATCATTTGGAACACTTGTTATTTTGGGCTTATCGGGGCCCA
65 ATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATC-GGGCCCA
1885 TTAGTTCCGTTTTGAATCGTCTTCG
129 TTAGTTCCGTTTTGAATCGTCTTCG
* * *
1910 ATTTGGGAAATCTCAATGCTTTTCTTTCCAATGTTTATGGCCTAACTATAATCATTTTTGTGAGA
1 ATTTGGGAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGA
* *
1975 TTAGTCCACTCTGAAGTTTTTAGCTCACTTGGAACACTTGTTATTTTGGG-----C---CCCATT
66 TTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGCCCATT
*
2032 AGTTCCGTATTGAATCGTCTTCG
131 AGTTCCGTTTTGAATCGTCTTCG
* * * *
2055 ATTTGGGAAACCTTAATGCTTTTCTTTCTATTGATTATGGCCTAACTATAATCATTTTGGTGAGC
1 ATTTGGGAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGA
* * * *
2120 TTAGTCCACTGTGAAGTTTTTAGCTCATTTGTAACACTTGTTTTTTTGGGCCTAACGGGCCCTTT
66 TTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGCCCATT
***
2185 AGTGAAGTTTTGAATCGTCTTCG
131 AGTTCCGTTTTGAATCGTCTTCG
* *
2208 ATTTGGCAAACCTCAATGCTTTTCTTTCCATTGATTATGGCCTAACTATAATCATTTTGGTGAGA
1 ATTTGGGAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGA
* *
2273 TTAGTCCACTGTGAAGTTTTTCGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGCCCACT
66 TTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGCCCATT
*
2338 AGTTCCGTTTTGAATCGTCTTCA
131 AGTTCCGTTTTGAATCGTCTTCG
* * * * * *
2361 ACTTGGCAACCCTCAATTCTTTTCTTTCCATTGTTTATGCCCTAAC-AGTAATCATTATGGTGAG
1 ATTTGGGAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTA-TAATCATTTTGGTGAG
* * *
2425 ATTAGTCCACTTTGAAGTTTTTAACTCATTTGGAACACTTGTTACTTTGGGCCTATCGGGCCCAT
65 ATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGCCCAT
** *
2490 TAGTGACATTTTGAATCGTCTTCG
130 TAGTTCCGTTTTGAATCGTCTTCG
* * *
2514 ATTTGGGAAACCTCAATGCTTTTCGTTCCATTGATTATCGCCTAACTATAATCATTTTGGTGAGA
1 ATTTGGGAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGA
* * * *
2579 TTAGTCCACTGTAAAGTTTTTAGCTCATTTGGAACACTTGTTATTTAGGGACTATCAAGGCCCAT
66 TTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATC-GGGCCCAT
2644 TAGTTCCGTTTTGAATCGTCTTCG
130 TAGTTCCGTTTTGAATCGTCTTCG
* **
2668 ATTTCGGAAACCTCAATGCTTTTCTACCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGA
1 ATTTGGGAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGA
* * *
2733 TTAGTCCACTGTGAAGTTTTTAACTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGACCACT
66 TTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGCCCATT
* *
2798 AGTTCCGGTTTGATTCGTCTTCG
131 AGTTCCGTTTTGAATCGTCTTCG
* * * * * * *
2821 ACTTGGCAACCCTCAATTCTTTTCTTTCCATTGTTTATGTCCTAACTGTAATCATTATGGTGAGA
1 ATTTGGGAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGA
*
2886 TTAGTCCACTTTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGACCCAT
66 TTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGG-CCCAT
*
2951 TACTTCCGTTTTGAATCGTCTTCG
130 TAGTTCCGTTTTGAATCGTCTTCG
* * *
2975 ATTTGGGAAACCTCAATGCTTTTC-TCCCATTCTTTATGGCCTAACTATAATTATTTTGGTGAGA
1 ATTTGGGAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGA
*
3039 TTAGTCCACTGTGAAGTTTTTAGCTTATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCAT
66 TTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATC-GGGCCCAT
*
3104 TAGTACCGTTTTGAATCGTCTTCG
130 TAGTTCCGTTTTGAATCGTCTTCG
* * * *
3128 ACTTGGGAAACCTTAATGCTTTTCTTTCCATTGATTATGCCCTAACTATAATCATTTTGGTGAGA
1 ATTTGGGAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGA
*
3193 TTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCTTATCGGGGCCCAT
66 TTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATC-GGGCCCAT
3258 TAGTTCCGTTTTGAATCGTCTTCG
130 TAGTTCCGTTTTGAATCGTCTTCG
* * * *
3282 ATTTGGCAAACCTCGATGCTTTTCTTTCTATTGTTTATGGCCTAACTATAATCATTATGGTGAGA
1 ATTTGGGAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGA
** * *
3347 TTAGTCCACTGTGAAGCGTTTAGCTCATTTGGAACATTTGTTATTTTGGGCCTATCGGGCCCACT
66 TTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGCCCATT
3412 AGTTCCGTTTTGAATCGTCTTCG
131 AGTTCCGTTTTGAATCGTCTTCG
* *
3435 ATTTGGGAAACCTCAATTCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTATGGTGAGA
1 ATTTGGGAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGA
* * * * *
3500 TTAGTCCTCTTTGAAATTTTTAACTCATTTGGAACACTTGTTACTTTGGGCCTATCGGGTCCCAT
66 TTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGG-CCCAT
* ** *
3565 CAGTGACATTTTGAATCGTCTTCG
130 TAGTTCCGTTTTGAATCGTCTTCG
*
3589 ATTTGGGAAACCTCAATGCTTTTCTTTCCATTGATTATGGCCTAACTATAATCATTTTGGTGAGA
1 ATTTGGGAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGA
3654 TTAGTCCA
66 TTAGTCCA
3662 TGTCGTAACG
Statistics
Matches: 2394, Mismatches: 250, Indels: 59
0.89 0.09 0.02
Matches are distributed among these distances:
145 132 0.06
149 1 0.00
150 1 0.00
151 3 0.00
152 44 0.02
153 1282 0.54
154 875 0.37
155 25 0.01
156 18 0.01
157 13 0.01
ACGTcount: A:0.22, C:0.19, G:0.18, T:0.40
Consensus pattern (153 bp):
ATTTGGGAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGA
TTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGCCCATT
AGTTCCGTTTTGAATCGTCTTCG
Found at i:1460 original size:307 final size:307
Alignment explanation
Indices: 833--3661 Score: 4121
Period size: 307 Copynumber: 9.2 Consensus size: 307
823 ATTTGGAACA
* *
833 ATTTGGGAAACCTCGAATTGC-TTGCTTTCCATTGTTTACTGGCGTAACTATAATCATTTTAGGT
1 ATTTGGGAAACCTC-AA-TGCTTTTCTTTCCATTGTTTA-TGGCCTAACTATAATCATTTT-GGT
* * *
897 GAGATTAGACCACTGTGAAGTTTTTAGATCATTTGGAACACTTGTTATTTTGGACCTATCGGGGC
62 GAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATC-GGGC
* *
962 CCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGGAAACCCCAATGCTTTTCTTTCCATTGTTTA
126 CCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTA
*
1027 TGGCCTAACTATAATCATTTTTGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACAC
191 TGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACAC
1092 TTG-TATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCG
256 TTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCG
* * *
1143 ATTTGGGAAACATCAATGCTTTTCGTTCCATTGATTATGGCCTAACTATAATCATTTTGGTGAGA
1 ATTTGGGAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGA
* * *
1208 TTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTCTTATCTTGGGCCTATCGGGCCCACT
66 TTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGCCCATT
* * * * *
1273 ACTTCCGTTTTGAATCATCTTCGACTTGGCAACCCTCAATTCTTTGT-TTTCCATTGTTTATGGC
131 AGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTT-TCTTTCCATTGTTTATGGC
* * * *
1337 CTAACTGTAATCATTATGGTGAGATTAGTCCACTTTGAAGTTTTTAACTCATTTGGAACACTTGT
195 CTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGT
* * * ** * *
1402 TATTTTGGGCCAATCAGGCCCCATTAGTGACATTTTGAATAGTCTTCG
260 TATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCG
*
1450 ATTTGGGAAACCTCAATGCTTTTCTTT-CATTGATTATGGCCTAACTATAATCATTTTGGTGAGA
1 ATTTGGGAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGA
* *
1514 TTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTAGACCTATCGGGCCCATT
66 TTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGCCCATT
* *
1579 AGTTCCGTTTTGAATCGTCTTCGACTTT-GC-TACTCTCAATTCTTTTCTTTCCATTGTTTATGG
131 AGTTCCGTTTTGAATCGTCTTCGA-TTTGGCAAAC-CTCAATGCTTTTCTTTCCATTGTTTATGG
* * *
1642 CCTAACTGTAATCATTATCGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTG
194 CCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTG
* * * * *
1707 TTATTTTGGACCTATCAGGGCCTATTAGATCTGTTTTGAATCGTCTTCG
259 TTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCG
* * * *
1756 ATTTGGCAACCCTCAATGTTTTTCTTTCCATTGTTTATGGCCTAAC-AGTAATCATTATGGTGAG
1 ATTTGGGAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTA-TAATCATTTTGGTGAG
* * * *
1820 ATTAGTCCACTTTGAAGATTTTAGATCATTTGGAACACTTGTTATTTTGGGCTTATCGGGGCCCA
65 ATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATC-GGGCCCA
* * *
1885 TTAGTTCCGTTTTGAATCGTCTTCGATTTGGGAAATCTCAATGCTTTTCTTTCCAATGTTTATGG
129 TTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGG
* * *
1950 CCTAACTATAATCATTTTTGTGAGATTAGTCCACTCTGAAGTTTTTAGCTCACTTGGAACACTTG
194 CCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTG
*
2015 TTATTTTGGG-----C----CCCATTAGTTCCGTATTGAATCGTCTTCG
259 TTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCG
* * * *
2055 ATTTGGGAAACCTTAATGCTTTTCTTTCTATTGATTATGGCCTAACTATAATCATTTTGGTGAGC
1 ATTTGGGAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGA
* * * *
2120 TTAGTCCACTGTGAAGTTTTTAGCTCATTTGTAACACTTGTTTTTTTGGGCCTAACGGGCCCTTT
66 TTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGCCCATT
*** *
2185 AGTGAAGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGATTATGGCC
131 AGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCC
*
2250 TAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTCGCTCATTTGGAACACTTGTT
196 TAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTT
* *
2315 ATTTTGGGCCTATC-GGGCCCACTAGTTCCGTTTTGAATCGTCTTCA
261 ATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCG
* * * * * *
2361 ACTTGGCAACCCTCAATTCTTTTCTTTCCATTGTTTATGCCCTAAC-AGTAATCATTATGGTGAG
1 ATTTGGGAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTA-TAATCATTTTGGTGAG
* * *
2425 ATTAGTCCACTTTGAAGTTTTTAACTCATTTGGAACACTTGTTACTTTGGGCCTATCGGGCCCAT
65 ATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGCCCAT
** * * * * *
2490 TAGTGACATTTTGAATCGTCTTCGATTTGGGAAACCTCAATGCTTTTCGTTCCATTGATTATCGC
130 TAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGC
*
2555 CTAACTATAATCATTTTGGTGAGATTAGTCCACTGTAAAGTTTTTAGCTCATTTGGAACACTTGT
195 CTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGT
* * **
2620 TATTTAGGGACTATCAAGGCCCATTAGTTCCGTTTTGAATCGTCTTCG
260 TATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCG
* **
2668 ATTTCGGAAACCTCAATGCTTTTCTACCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGA
1 ATTTGGGAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGA
* * *
2733 TTAGTCCACTGTGAAGTTTTTAACTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGACCACT
66 TTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGCCCATT
* * * * * *
2798 AGTTCCGGTTTGATTCGTCTTCGACTTGGCAACCCTCAATTCTTTTCTTTCCATTGTTTATGTCC
131 AGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCC
* * *
2863 TAACTGTAATCATTATGGTGAGATTAGTCCACTTTGAAGTTTTTAGCTCATTTGGAACACTTGTT
196 TAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTT
* *
2928 ATTTTGGGCCTATCGGGACCCATTACTTCCGTTTTGAATCGTCTTCG
261 ATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCG
* * *
2975 ATTTGGGAAACCTCAATGCTTTTC-TCCCATTCTTTATGGCCTAACTATAATTATTTTGGTGAGA
1 ATTTGGGAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGA
*
3039 TTAGTCCACTGTGAAGTTTTTAGCTTATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCAT
66 TTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATC-GGGCCCAT
* * * * * *
3104 TAGTACCGTTTTGAATCGTCTTCGACTTGGGAAACCTTAATGCTTTTCTTTCCATTGATTATGCC
130 TAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGC
3169 CTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGT
195 CTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGT
*
3234 TATTTTGGGCTTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCG
260 TATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCG
* * * *
3282 ATTTGGCAAACCTCGATGCTTTTCTTTCTATTGTTTATGGCCTAACTATAATCATTATGGTGAGA
1 ATTTGGGAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGA
** * *
3347 TTAGTCCACTGTGAAGCGTTTAGCTCATTTGGAACATTTGTTATTTTGGGCCTATCGGGCCCACT
66 TTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGCCCATT
* *
3412 AGTTCCGTTTTGAATCGTCTTCGATTTGGGAAACCTCAATTCTTTTCTTTCCATTGTTTATGGCC
131 AGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCC
* * * * *
3477 TAACTATAATCATTATGGTGAGATTAGTCCTCTTTGAAATTTTTAACTCATTTGGAACACTTGTT
196 TAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTT
* * * ** *
3542 ACTTTGGGCCTATCGGGTCCCATCAGTGACATTTTGAATCGTCTTCG
261 ATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCG
*
3589 ATTTGGGAAACCTCAATGCTTTTCTTTCCATTGATTATGGCCTAACTATAATCATTTTGGTGAGA
1 ATTTGGGAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGA
3654 TTAGTCCA
66 TTAGTCCA
3662 TGTCGTAACG
Statistics
Matches: 2260, Mismatches: 234, Indels: 53
0.89 0.09 0.02
Matches are distributed among these distances:
298 135 0.06
299 129 0.06
300 1 0.00
303 2 0.00
305 3 0.00
306 759 0.34
307 960 0.42
308 241 0.11
309 17 0.01
310 13 0.01
ACGTcount: A:0.22, C:0.19, G:0.18, T:0.40
Consensus pattern (307 bp):
ATTTGGGAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGA
TTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGCCCATT
AGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCC
TAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTT
ATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCG
Found at i:1801 original size:460 final size:459
Alignment explanation
Indices: 833--3661 Score: 4068
Period size: 460 Copynumber: 6.2 Consensus size: 459
823 ATTTGGAACA
* * *
833 ATTTGGGAAACCTCGAATTGC-TTGCTTTCCATTGTTTACTGGCGTAACTATAATCATTTTAGGT
1 ATTTGGCAAACCTC-AA-TGCTTTTCTTTCCATTGTTTA-TGGCCTAACTATAATCATTTT-GGT
* *
897 GAGATTAGACCACTGTGAAGTTTTTAGA-TCATTTGGAACACTTGTTATTTTGGACCTATCGGGG
62 GAGATTAGTCCACTGTGAAGTTTTTA-ACTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGG
* *
961 CCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGGAAACCCCAATGCTTTTCTTTCCATTGTTT
126 CCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTT
* *
1026 ATGGCCTAACTATAATCATTTTTGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACA
191 ATGGCCTAACTATAATCATTATGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACA
*
1091 CTTG-TATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGGAAACA
256 CTTGTTATTTTGGGCCTATC-GGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTT-GGAAACC
*
1155 TCAATGCTTTTCGTTCCATTGATTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGT
319 TCAATGCTTTTCTTTCCATTGATTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGT
* * * * *
1220 GAAGTTTTTAGCTCATTTGGAACACTTCTTATCTTGGGCCTATCGGGCCCACTACTTCCGTTTTG
384 GAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGCCCATTAGTACCGTTTTG
*
1285 AATCATCTTCG
449 AATCGTCTTCG
* * * * *
1296 ACTTGGCAACCCTCAATTCTTTGT-TTTCCATTGTTTATGGCCTAACTGTAATCATTATGGTGAG
1 ATTTGGCAAACCTCAATGCTTT-TCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAG
* * * *
1360 ATTAGTCCACTTTGAAGTTTTTAACTCATTTGGAACACTTGTTATTTTGGGCCAATCAGGCCCCA
65 ATTAGTCCACTGTGAAGTTTTTAACTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCA
** * * * *
1425 TTAGTGACATTTTGAATAGTCTTCGATTTGGGAAACCTCAATGCTTTTCTTT-CATTGATTATGG
130 TTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGG
*
1489 CCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTG
195 CCTAACTATAATCATTATGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTG
* * **
1554 TTATTTTAGACCTATCGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGACTTT-GCTACTCTCAA
260 TTATTTTGGGCCTATCGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGA-TTTGGAAAC-CTCAA
* * * * *
1618 TTCTTTTCTTTCCATTGTTTATGGCCTAACTGTAATCATTATCGTGAGATTAGTCCACTGTGAAG
323 TGCTTTTCTTTCCATTGATTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAG
* * *
1683 TTTTTAGCTCATTTGGAACACTTGTTATTTTGGACCTATCAGGGCCTATTAG-ATCTGTTTTGAA
388 TTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATC-GGGCCCATTAGTA-CCGTTTTGAA
1747 TCGTCTTCG
451 TCGTCTTCG
* * *
1756 ATTTGGCAACCCTCAATGTTTTTCTTTCCATTGTTTATGGCCTAAC-AGTAATCATTATGGTGAG
1 ATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTA-TAATCATTTTGGTGAG
* * *
1820 ATTAGTCCACTTTGAAGATTTTAGA-TCATTTGGAACACTTGTTATTTTGGGCTTATCGGGGCCC
65 ATTAGTCCACTGTGAAGTTTTTA-ACTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCC
* * *
1884 ATTAGTTCCGTTTTGAATCGTCTTCGATTTGGGAAATCTCAATGCTTTTCTTTCCAATGTTTATG
129 ATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATG
* * * *
1949 GCCTAACTATAATCATTTTTGTGAGATTAGTCCACTCTGAAGTTTTTAGCTCACTTGGAACACTT
194 GCCTAACTATAATCATTATGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTT
* *
2014 GTTATTTTGGG-----C---CCCATTAGTTCCGTATTGAATCGTCTTCGATTTGGGAAACCTTAA
259 GTTATTTTGGGCCTATCGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTT-GGAAACCTCAA
* *
2071 TGCTTTTCTTTCTATTGATTATGGCCTAACTATAATCATTTTGGTGAGCTTAGTCCACTGTGAAG
323 TGCTTTTCTTTCCATTGATTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAG
* * * * *
2136 TTTTTAGCTCATTTGTAACACTTGTTTTTTTGGGCCTAACGGGCCCTTTAGTGA-AGTTTTGAAT
388 TTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGCCCATTAGT-ACCGTTTTGAAT
2200 CGTCTTCG
452 CGTCTTCG
*
2208 ATTTGGCAAACCTCAATGCTTTTCTTTCCATTGATTATGGCCTAACTATAATCATTTTGGTGAGA
1 ATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGA
** *
2273 TTAGTCCACTGTGAAGTTTTTCGCTCATTTGGAACACTTGTTATTTTGGGCCTATC-GGGCCCAC
66 TTAGTCCACTGTGAAGTTTTTAACTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCAT
* * * * *
2337 TAGTTCCGTTTTGAATCGTCTTCAACTTGGCAACCCTCAATTCTTTTCTTTCCATTGTTTATGCC
131 TAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGC
* *
2402 CTAAC-AGTAATCATTATGGTGAGATTAGTCCACTTTGAAGTTTTTAACTCATTTGGAACACTTG
196 CTAACTA-TAATCATTATGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTG
* ** *
2466 TTACTTTGGGCCTATCGGGCCCATTAGTGACATTTTGAATCGTCTTCGATTTGGGAAACCTCAAT
260 TTATTTTGGGCCTATCGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTT-GGAAACCTCAAT
* * *
2531 GCTTTTCGTTCCATTGATTATCGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTAAAGT
324 GCTTTTCTTTCCATTGATTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGT
* * * *
2596 TTTTAGCTCATTTGGAACACTTGTTATTTAGGGACTATCAAGGCCCATTAGTTCCGTTTTGAATC
389 TTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATC-GGGCCCATTAGTACCGTTTTGAATC
2661 GTCTTCG
453 GTCTTCG
**
2668 ATTTCGG-AAACCTCAATGCTTTTCTACCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAG
1 ATTT-GGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAG
*
2732 ATTAGTCCACTGTGAAGTTTTTAACTCATTTGGAACACTTGTTATTTTGGGCCTATC-GGGACCA
65 ATTAGTCCACTGTGAAGTTTTTAACTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCA
* * * * * * *
2796 CTAGTTCCGGTTTGATTCGTCTTCGACTTGGCAACCCTCAATTCTTTTCTTTCCATTGTTTATGT
130 TTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGG
* *
2861 CCTAACTGTAATCATTATGGTGAGATTAGTCCACTTTGAAGTTTTTAGCTCATTTGGAACACTTG
195 CCTAACTATAATCATTATGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTG
*
2926 TTATTTTGGGCCTATCGGGACCCATTACTTCCGTTTTGAATCGTCTTCGATTTGGGAAACCTCAA
260 TTATTTTGGGCCTATCGGG-CCCATTAGTTCCGTTTTGAATCGTCTTCGATTT-GGAAACCTCAA
* ** *
2991 TGCTTTTC-TCCCATTCTTTATGGCCTAACTATAATTATTTTGGTGAGATTAGTCCACTGTGAAG
323 TGCTTTTCTTTCCATTGATTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAG
*
3055 TTTTTAGCTTATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTACCGTTTTGAAT
388 TTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATC-GGGCCCATTAGTACCGTTTTGAAT
3120 CGTCTTCG
452 CGTCTTCG
* * * * *
3128 ACTTGGGAAACCTTAATGCTTTTCTTTCCATTGATTATGCCCTAACTATAATCATTTTGGTGAGA
1 ATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGA
* *
3193 TTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCTTATCGGGGCCCAT
66 TTAGTCCACTGTGAAGTTTTTAACTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCAT
* *
3258 TAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCGATGCTTTTCTTTCTATTGTTTATGGC
131 TAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGC
** *
3323 CTAACTATAATCATTATGGTGAGATTAGTCCACTGTGAAGCGTTTAGCTCATTTGGAACATTTGT
196 CTAACTATAATCATTATGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGT
* *
3388 TATTTTGGGCCTATCGGGCCCACTAGTTCCGTTTTGAATCGTCTTCGATTTGGGAAACCTCAATT
261 TATTTTGGGCCTATCGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTT-GGAAACCTCAATG
* * * * *
3453 CTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTATGGTGAGATTAGTCCTCTTTGAAATT
325 CTTTTCTTTCCATTGATTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTT
* * * *
3518 TTTAACTCATTTGGAACACTTGTTACTTTGGGCCTATCGGGTCCCATCAGTGA-CATTTTGAATC
390 TTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGG-CCCATTAGT-ACCGTTTTGAATC
3582 GTCTTCG
453 GTCTTCG
* *
3589 ATTTGGGAAACCTCAATGCTTTTCTTTCCATTGATTATGGCCTAACTATAATCATTTTGGTGAGA
1 ATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGA
3654 TTAGTCCA
66 TTAGTCCA
3662 TGTCGTAACG
Statistics
Matches: 2136, Mismatches: 193, Indels: 76
0.89 0.08 0.03
Matches are distributed among these distances:
450 1 0.00
451 130 0.06
452 138 0.06
453 128 0.06
454 4 0.00
456 2 0.00
458 3 0.00
459 347 0.16
460 880 0.41
461 474 0.22
462 18 0.01
463 11 0.01
ACGTcount: A:0.22, C:0.19, G:0.18, T:0.40
Consensus pattern (459 bp):
ATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGA
TTAGTCCACTGTGAAGTTTTTAACTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCAT
TAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGC
CTAACTATAATCATTATGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGT
TATTTTGGGCCTATCGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGAAACCTCAATGC
TTTTCTTTCCATTGATTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTT
TTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGCCCATTAGTACCGTTTTGAATCGTC
TTCG
Found at i:4124 original size:4 final size:4
Alignment explanation
Indices: 4115--4361 Score: 97
Period size: 4 Copynumber: 62.8 Consensus size: 4
4105 TAATAATAAT
* ** * *
4115 AATA AATA AATA GAT- AATA GCTA AATT AATA AATA AGA-A GATA AAT-
1 AATA AATA AATA AATA AATA AATA AATA AATA AATA A-ATA AATA AATA
* * * *
4161 AGTA AATA AATA GAT- AATA ATTA AATT AATA AATA AA-A AGATA AAT-
1 AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA A-ATA AATA
* * * * *
4207 AGTA AATA AATA GATA ATAGTT AA-A AATA AATA AATA GATA AAT- AGTA
1 AATA AATA AATA AATA A-A-TA AATA AATA AATA AATA AATA AATA AATA
* * * * *
4255 AATA AATA GATA ATAGTT AA-A AATA AATA AATT GATA AAT- AGTA AATA
1 AATA AATA AATA A-A-TA AATA AATA AATA AATA AATA AATA AATA AATA
* * * * *
4303 AATA GATGA TAGTT AA-A AATA AATA AATAA AATA AAT- AGTG AATA AAT-
1 AATA AAT-A -AATA AATA AATA AATA AAT-A AATA AATA AATA AATA AATA
*
4351 AATA AAAA AAT
1 AATA AATA AAT
4362 CTTTTTGGTC
Statistics
Matches: 172, Mismatches: 49, Indels: 44
0.65 0.18 0.17
Matches are distributed among these distances:
3 26 0.15
4 129 0.75
5 12 0.07
6 5 0.03
ACGTcount: A:0.64, C:0.00, G:0.09, T:0.27
Consensus pattern (4 bp):
AATA
Found at i:4144 original size:27 final size:26
Alignment explanation
Indices: 4094--4252 Score: 99
Period size: 27 Copynumber: 6.4 Consensus size: 26
4084 AATAGGTAGC
* *
4094 TAAA-AAAAAGATAATAAT-AA-TAA
1 TAAATAAATAGATAATAGTAAATTAA
4117 TAAATAAATAGATAATAGCTAAATTAA
1 TAAATAAATAGATAATAG-TAAATTAA
4144 TAAATAAGA-AGATAAATAGT--A--AA
1 TAAATAA-ATAGAT-AATAGTAAATTAA
*
4167 TAAATAGATA-ATAAT--TAAATTAA
1 TAAATAAATAGATAATAGTAAATTAA
* *
4190 TAAATAAAAAGATAAATAGTAAATAAA
1 TAAATAAATAGAT-AATAGTAAATTAA
* * * * *
4217 TAGAT-AATAGTTAAAAATAAATAAA
1 TAAATAAATAGATAATAGTAAATTAA
*
4242 TAGATAAATAG
1 TAAATAAATAG
4253 TAAATAAATA
Statistics
Matches: 109, Mismatches: 11, Indels: 29
0.73 0.07 0.19
Matches are distributed among these distances:
19 1 0.01
21 4 0.04
22 3 0.03
23 23 0.21
24 13 0.12
25 21 0.19
26 12 0.11
27 26 0.24
28 6 0.06
ACGTcount: A:0.65, C:0.01, G:0.08, T:0.26
Consensus pattern (26 bp):
TAAATAAATAGATAATAGTAAATTAA
Found at i:4251 original size:44 final size:44
Alignment explanation
Indices: 4048--4355 Score: 349
Period size: 44 Copynumber: 6.9 Consensus size: 44
4038 TAAAATAATA
* * * * *
4048 AAAAAAAAGATAAATAGATACAA-AGAATAATAAATAAATAGGTAGCT
1 AAAAATAA-ATAAATAGATA-AATAGTA-AATAAATAGATA-ATAGTT
* * *
4095 AAAAA-AAAGATAATA-AT-AATAATAAATAAATAGATAATAGCT
1 AAAAATAAATA-AATAGATAAATAGTAAATAAATAGATAATAGTT
*
4137 AAATTAATAAATAAGA-AGATAAATAGTAAATAAATAGATAATAATT
1 AAA--AATAAATAA-ATAGATAAATAGTAAATAAATAGATAATAGTT
*
4183 AAATTAATAAATAAAAAGATAAATAGTAAATAAATAGATAATAGTT
1 AAA--AATAAATAAATAGATAAATAGTAAATAAATAGATAATAGTT
4229 AAAAATAAATAAATAGATAAATAGTAAATAAATAGATAATAGTT
1 AAAAATAAATAAATAGATAAATAGTAAATAAATAGATAATAGTT
* *
4273 AAAAATAAATAAATTGATAAATAGTAAATAAATAGATGATAGTT
1 AAAAATAAATAAATAGATAAATAGTAAATAAATAGATAATAGTT
* *
4317 AAAAATAAATAAATAAAATAAATAGTGAATAAATA-ATAA
1 AAAAATAAATAAAT-AGATAAATAGTAAATAAATAGATAA
4356 AAAAATCTTT
Statistics
Matches: 234, Mismatches: 17, Indels: 23
0.85 0.06 0.08
Matches are distributed among these distances:
42 8 0.03
43 13 0.06
44 105 0.45
45 29 0.12
46 74 0.32
47 5 0.02
ACGTcount: A:0.64, C:0.01, G:0.09, T:0.26
Consensus pattern (44 bp):
AAAAATAAATAAATAGATAAATAGTAAATAAATAGATAATAGTT
Found at i:4264 original size:19 final size:19
Alignment explanation
Indices: 4130--4341 Score: 117
Period size: 19 Copynumber: 11.3 Consensus size: 19
4120 ATAAATAGAT
* *
4130 AATAGCTAAATTAATAAATA
1 AATAGATAAA-TAGTAAATA
4150 AGA-AGATAAATAGTAAATA
1 A-ATAGATAAATAGTAAATA
* *
4169 AATAGAT-AATAATTAAATT
1 AATAGATAAAT-AGTAAATA
* *
4188 AATAAATAAA-A--AGATA
1 AATAGATAAATAGTAAATA
* *
4204 AATAG-TAAATAAATAGAT-
1 AATAGATAAAT-AGTAAATA
* *
4222 AATAGTTAAA-AATAAATA
1 AATAGATAAATAGTAAATA
4240 AATAGATAAATAGTAAATA
1 AATAGATAAATAGTAAATA
4259 AATAGAT-AATAGTTAAAAATA
1 AATAGATAAATAG-T--AAATA
4280 AATAAATTGATAAATAGTAAATA
1 AAT--A--GATAAATAGTAAATA
* *
4303 AATAGAT-GATAGTTAA-A
1 AATAGATAAATAGTAAATA
*
4320 AATAAATAAATA--AAATA
1 AATAGATAAATAGTAAATA
4337 AATAG
1 AATAG
4342 TGAATAAATA
Statistics
Matches: 154, Mismatches: 17, Indels: 45
0.71 0.08 0.21
Matches are distributed among these distances:
15 4 0.03
16 9 0.06
17 19 0.12
18 34 0.22
19 51 0.33
20 9 0.06
21 10 0.06
23 9 0.06
25 4 0.03
26 5 0.03
ACGTcount: A:0.63, C:0.00, G:0.09, T:0.27
Consensus pattern (19 bp):
AATAGATAAATAGTAAATA
Found at i:5918 original size:35 final size:35
Alignment explanation
Indices: 5873--6228 Score: 455
Period size: 35 Copynumber: 10.0 Consensus size: 35
5863 ATCAATGTGA
*
5873 AGATCAACTCTGATCATCGAAAACTTCTTGAAATA
1 AGATCAACTCTGATCATCGAAAACTTCTTGAAATG
** *
5908 AGATCAACTCTGATCATAAAAAAGAACTTCTTGAAAGG
1 AGATCAACTCTGATCAT--CGAA-AACTTCTTGAAATG
* **
5946 AGATCAACTCTGACCATATAAAAAACTTCTTGAAATG
1 AGATCAACTCTGATC--ATCGAAAACTTCTTGAAATG
* *
5983 AGATCAACTCTGATCAACGAAAAC-TCTTTGAAACG
1 AGATCAACTCTGATCATCGAAAACTTC-TTGAAATG
6018 AGATCAACTCTGATCATCGAAAACTTCTTGAAATG
1 AGATCAACTCTGATCATCGAAAACTTCTTGAAATG
* * * *
6053 ATATCAACTCTGACCAT-AAAAACATCTTGAAAATG
1 AGATCAACTCTGATCATCGAAAACTTCTTG-AAATG
** * *
6088 AGATCAACTCTGATCATAAAAAACTTCCTGAAAGG
1 AGATCAACTCTGATCATCGAAAACTTCTTGAAATG
*
6123 AGATCAACTCTGATCACCGAAAACTTCTTGAAATG
1 AGATCAACTCTGATCATCGAAAACTTCTTGAAATG
*
6158 AGATCAACTCTGATCATCGAAAACTTCTTGAAACG
1 AGATCAACTCTGATCATCGAAAACTTCTTGAAATG
*
6193 AGATCAACTCTGATCATCGAAAACTTCTTGGAATG
1 AGATCAACTCTGATCATCGAAAACTTCTTGAAATG
6228 A
1 A
6229 CCGCACTGGA
Statistics
Matches: 281, Mismatches: 31, Indels: 18
0.85 0.09 0.05
Matches are distributed among these distances:
34 12 0.04
35 196 0.70
36 12 0.04
37 29 0.10
38 30 0.11
40 2 0.01
ACGTcount: A:0.40, C:0.20, G:0.13, T:0.26
Consensus pattern (35 bp):
AGATCAACTCTGATCATCGAAAACTTCTTGAAATG
Found at i:6275 original size:54 final size:54
Alignment explanation
Indices: 6193--6406 Score: 374
Period size: 54 Copynumber: 4.0 Consensus size: 54
6183 TCTTGAAACG
* *
6193 AGATCAACTCTGATCATCGAAAACTTCTTGGAATGACCGCACTGGATCATCTGA
1 AGATCAACTCTGACCATTGAAAACTTCTTGGAATGACCGCACTGGATCATCTGA
*
6247 AGATCAACTCTGACCATTGAAAACTTCTTGGAATGACCGCACTGGATCATCTCA
1 AGATCAACTCTGACCATTGAAAACTTCTTGGAATGACCGCACTGGATCATCTGA
* * *
6301 GGATCAACTCTGACCTTTGAAAACTTCTTGGAATGACCGCACTAGATCATCTGA
1 AGATCAACTCTGACCATTGAAAACTTCTTGGAATGACCGCACTGGATCATCTGA
6355 AGATCAACTCTGACCATTGAAAACTTCTTGGAATGACCGCACTGGATCATCT
1 AGATCAACTCTGACCATTGAAAACTTCTTGGAATGACCGCACTGGATCATCT
6407 AAACACCTGT
Statistics
Matches: 150, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
54 150 1.00
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.27
Consensus pattern (54 bp):
AGATCAACTCTGACCATTGAAAACTTCTTGGAATGACCGCACTGGATCATCTGA
Done.