Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01010847.1 Corchorus olitorius cultivar O-4 contig10879, 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: 3851
ACGTcount: A:0.25, C:0.21, G:0.17, T:0.36
Found at i:910 original size:154 final size:153
Alignment explanation
Indices: 630--1251 Score: 956
Period size: 154 Copynumber: 4.0 Consensus size: 153
620 ATCAACACTC
*
630 TTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCCTTTGGAACACTTGTTATTTTGGGCCTAT
1 TTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTAT
**
695 CGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAAACTCAATGCTTTTCTTTCCAT
66 CGGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGC-AAACTCAATGCTTTTCTTTCCAT
* *
760 TGTTTATGGCCTAACTATAATCAT
130 TATTTATGGACTAACTATAATCAT
*
784 TTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTTGAACACTTGTTATTTTGGGCCTAT
1 TTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTAT
* ** * *
849 TGGGGCCCATTAGTTCCGTTTTGAATAGTCTTCGATTTGGCAAATCTCAAAGCTTTTCTTTCCAT
66 CGGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAA-CTCAATGCTTTTCTTTCCAT
*
914 TATTTATGGACTAACTACAATCAT
130 TATTTATGGACTAACTATAATCAT
*
938 TTTGGTGAGATTAGTCCACTGTGAAGTTTTTATCTCATTTGGAACACTTGTTATTTTGGGCCTAT
1 TTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTAT
*
1003 CGGGGCCCATTAGTGACGTTTTGAATCGTCTTCGAGTTGGCAAACCTCAATGCTTTTCTTTCCAT
66 CGGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAA-CTCAATGCTTTTCTTTCCAT
* *
1068 TATATATGGACTAACTGTAATCAT
130 TATTTATGGACTAACTATAATCAT
* * * *
1092 TTTGGTGAGATTAGTCCACTATGATGTTTTTAGCTCATTCGGAACACTTGTTATTTTGGTCCTAT
1 TTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTAT
** * * * *
1157 CAAGGCCCATTAGTGACGTTTTGAATCGTCTTCAATTCGGCAAACCCTAATGCTTTTTCTTTTCA
66 CGGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACTC-AATGC-TTTTCTTTCCA
*
1222 TTGTTTATGGACTAACTATAATCAT
129 TTATTTATGGACTAACTATAATCAT
1247 TTTGG
1 TTTGG
1252 ATTTCGGGCC
Statistics
Matches: 430, Mismatches: 35, Indels: 5
0.91 0.07 0.01
Matches are distributed among these distances:
153 5 0.01
154 388 0.90
155 37 0.09
ACGTcount: A:0.22, C:0.18, G:0.19, T:0.41
Consensus pattern (153 bp):
TTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTAT
CGGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACTCAATGCTTTTCTTTCCATT
ATTTATGGACTAACTATAATCAT
Found at i:1463 original size:262 final size:262
Alignment explanation
Indices: 990--1464 Score: 765
Period size: 262 Copynumber: 1.8 Consensus size: 262
980 AACACTTGTT
* *
990 ATTTTGGGCCTATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTCGAGTTGGCAAACCTCAATG
1 ATTTCGGGCCTATCGAGGCCCATTAGTGACGTTTTGAATCGTCTTCGAGTTGGCAAACCTCAATG
* * *
1055 CTTTTCTTTCCATTATATATGGACTAACTGTAATCATTTTGGTGAGATTAGTCCACTATGATGTT
66 CTTTTCTTTCCATTATATATGGACTAACTATAATCATATTGGTGAGATTAGTCCACTATGAAGTT
*
1120 TTTAGCTCATTCGGAACACTTGTTATTTTGGTCCTATCAAGGCCCATTAGTGACGTTTTGAATCG
131 TTTAGCTCATTCGGAACACTTGTTATTTTGGGCCTATCAAGGCCCATTAGTGACGTTTTGAATCG
1185 TCTTCAATTCGGCAAACCCTAATGCTTTTTCTTTTCATTGTTTATGGACTAACTATAATCATTTT
196 TCTTCAATTCGGCAAACCCTAATGCTTTTTCTTTTCATTGTTTATGGACTAACTATAATCATTTT
1250 GG
261 GG
*
1252 ATTTCGGGCCTATCGAGGCCCATTAGTGACGTTTTGAATCGTCTTTGA-TTCGGCAAACC-CTAA
1 ATTTCGGGCCTATCGAGGCCCATTAGTGACGTTTTGAATCGTCTTCGAGTT-GGCAAACCTC-AA
* * * *
1315 TGCTTTTCTTTTCATTTTTTATGGACTAACTATAATCATATTGGTGAGATTAGTCCACTGTGAAG
64 TGCTTTTCTTTCCATTATATATGGACTAACTATAATCATATTGGTGAGATTAGTCCACTATGAAG
* **
1380 TTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTTTTGAAT
129 TTTTTAGCTCATTCGGAACACTTGTTATTTTGGGCCTATCAAGGCCCATTAGTGACGTTTTGAAT
* * *
1445 CTTCTTCGATTTGGCAAACC
194 CGTCTTCAATTCGGCAAACC
1465 TCAAAGTTGT
Statistics
Matches: 194, Mismatches: 17, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
261 3 0.02
262 191 0.98
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.40
Consensus pattern (262 bp):
ATTTCGGGCCTATCGAGGCCCATTAGTGACGTTTTGAATCGTCTTCGAGTTGGCAAACCTCAATG
CTTTTCTTTCCATTATATATGGACTAACTATAATCATATTGGTGAGATTAGTCCACTATGAAGTT
TTTAGCTCATTCGGAACACTTGTTATTTTGGGCCTATCAAGGCCCATTAGTGACGTTTTGAATCG
TCTTCAATTCGGCAAACCCTAATGCTTTTTCTTTTCATTGTTTATGGACTAACTATAATCATTTT
GG
Found at i:1617 original size:416 final size:415
Alignment explanation
Indices: 836--1666 Score: 1177
Period size: 416 Copynumber: 2.0 Consensus size: 415
826 AACACTTGTT
* * * ** * *
836 ATTTTGGGCCTATTGGGGCCCATTAGTTCCGTTTTGAATAGTCTTCGATTTGGCAAATCTCAAAG
1 ATTTCGGGCCTATCGAGGCCCATTAGTGACGTTTTGAATAGTCTTCGATTCGGCAAACCTCAAAG
*
901 CTTTTCTTTCCATTATTTATGGACTAACTACAATCATTTTGGTGAGATTAGTCCACTGTGAAGTT
66 CTTTTCTTTCCATTATTTATGGACTAACTACAATCATATTGGTGAGATTAGTCCACTGTGAAGTT
*
966 TTTATCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTTTTGAATCG
131 TTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTTTTGAATCG
* * * *
1031 TCTTCGAGTTGGCAAACCTCAATGCTTTTCTTTCCATTATATATGGACTAACTGTAATCATTTTG
196 TCTTCGAGTTGGCAAACCTCAAAGCTTTTCTTTCAATTATATATGGACTAACTATAATCATTGTG
* * ** *
1096 GTGAGATTAGTCCACTATGATGTTTTTAGCTCATTCGGAACACTTGTTATTTTGGTCCTATCAAG
261 ATGAGATTAGTCCACTATGAAGTTCCTAGCTCATTCGGAACACTTGTTATTTTAGTCCTATCAAG
*
1161 GCCCATTAGTGACGTTTTGAATCGTCTTCAATTCGGCAAACC-CTAATGCTTTTTCTTTTCATTG
326 GCCCATTAGTGACGTTTTGAATCGTCTTCAATTCGGCAAACCTC-AATGC-TTTTCTTTCCATTG
1225 TTTATGGACTAACTATAATCATTTTGG
389 TTTATGGACTAACTATAATCATTTTGG
* * *
1252 ATTTCGGGCCTATCGAGGCCCATTAGTGACGTTTTGAATCGTCTTTGATTCGGCAAACC-CTAAT
1 ATTTCGGGCCTATCGAGGCCCATTAGTGACGTTTTGAATAGTCTTCGATTCGGCAAACCTC-AAA
* * *
1316 GCTTTTCTTTTCATTTTTTATGGACTAACTATAATCATATTGGTGAGATTAGTCCACTGTGAAGT
65 GCTTTTCTTTCCATTATTTATGGACTAACTACAATCATATTGGTGAGATTAGTCCACTGTGAAGT
1381 TTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTTTTGAATC
130 TTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTTTTGAATC
* * * * * **
1446 TTCTTCGATTTGGCAAACCTCAAAG-TTGTTCTTT-AAGTTGTTTATGGCCTAGTTATAATCATT
195 GTCTTCGAGTTGGCAAACCTCAAAGCTT-TTCTTTCAA-TTATATATGGACTAACTATAATCATT
* * * * *
1509 GTGATGATATTAGTCCACTGTGAAGTTCCTAGTTCATTTGGAACACTTGTTATTTTAAG-CCTTT
258 GTGATGAGATTAGTCCACTATGAAGTTCCTAGCTCATTCGGAACACTTGTTATTTT-AGTCCTAT
** ** * *
1573 CGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCAT
322 CAAGGCCCATTAGTGACGTTTTGAATCGTCTTCAATTCGGCAAACCTCAATGCTTTTCTTTCCAT
*
1638 TGTTTATGGCCTAACTATAATCATTTTGG
387 TGTTTATGGACTAACTATAATCATTTTGG
1667 TGAGATTAGT
Statistics
Matches: 366, Mismatches: 44, Indels: 11
0.87 0.10 0.03
Matches are distributed among these distances:
415 43 0.12
416 321 0.88
417 2 0.01
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.41
Consensus pattern (415 bp):
ATTTCGGGCCTATCGAGGCCCATTAGTGACGTTTTGAATAGTCTTCGATTCGGCAAACCTCAAAG
CTTTTCTTTCCATTATTTATGGACTAACTACAATCATATTGGTGAGATTAGTCCACTGTGAAGTT
TTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTTTTGAATCG
TCTTCGAGTTGGCAAACCTCAAAGCTTTTCTTTCAATTATATATGGACTAACTATAATCATTGTG
ATGAGATTAGTCCACTATGAAGTTCCTAGCTCATTCGGAACACTTGTTATTTTAGTCCTATCAAG
GCCCATTAGTGACGTTTTGAATCGTCTTCAATTCGGCAAACCTCAATGCTTTTCTTTCCATTGTT
TATGGACTAACTATAATCATTTTGG
Found at i:1767 original size:570 final size:569
Alignment explanation
Indices: 682--1840 Score: 1813
Period size: 570 Copynumber: 2.0 Consensus size: 569
672 AACACTTGTT
* ** *
682 ATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAAACTCAATG
1 ATTTAGGGCCTATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTCGGCAAAACTCAATG
* *
747 CTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTT
66 CTTTTCTTTCCATTGTTTATGGACTAACTATAATCATATTGGTGAGATTAGTCCACTGTGAAGTT
* * **
812 TTTAGCTCATTTTGAACACTTGTTATTTTGGGCCTATTGGGGCCCATTAGTTCCGTTTTGAATAG
131 TTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTTTTGAATAG
* * *
877 TCTTCGATTTGGCAAATCTCAAAGCTTTTCTTTCCATTATTTATGGACTAACTACAATCATTTTG
196 TCTTCGATTTGGCAAACCTCAAAGCTTTTCTTTCAATTATTTATGGACTAACTACAATCATTGTG
* ** **
942 GTGAGATTAGTCCACTGTGAAGTTTTTATCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGG
261 ATGAGATTAGTCCACTGTGAAGTTCCTATCTCATTTGGAACACTTGTTATTTTAAGCCTATCGGG
1007 GCCCATTAGTGACGTTTTGAATCGTCTTCGAGTTGGCAAACCTCAATGCTTTTCTTTCCATTATA
326 GCCCATTAGTGACGTTTTGAATCGTCTTCGAGTTGGCAAACCTCAATGCTTTTCTTTCCATTATA
* *
1072 TATGGACTAACTGTAATCATTTTGGTGAGATTAGTCCACTATGATGTTTTTAGCTCATTCGGAAC
391 TATGGACTAACTATAATCATTTTGGTGAGATTAGTCCACTATGAAGTTTTTAGCTCATTCGGAAC
*
1137 ACTTGTTATTTTGGTCCTATCAAGGCCCATTAGTGACGTTTTGAATCGTCTTCAATTCGGCAAAC
456 ACTTGTTATTTTGGGCCTATCAAGGCCCATTAGTGACGTTTTGAATCGTCTTCAATTCGGCAAAC
1202 CCTAATGCTTTTTCTTTTCATTGTTTATGGACTAACTATAATCATTTTGG
521 CCTAATGC-TTTTCTTTTCATTGTTTATGGACTAACTATAATCATTTTGG
* * * *
1252 ATTTCGGGCCTATCGAGGCCCATTAGTGACGTTTTGAATCGTCTTTGATTCGGC-AAACCCTAAT
1 ATTTAGGGCCTATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTCGGCAAAACTC-AAT
* *
1316 GCTTTTCTTTTCATTTTTTATGGACTAACTATAATCATATTGGTGAGATTAGTCCACTGTGAAGT
65 GCTTTTCTTTCCATTGTTTATGGACTAACTATAATCATATTGGTGAGATTAGTCCACTGTGAAGT
*
1381 TTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTTTTGAATC
130 TTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTTTTGAATA
* * * ** *
1446 TTCTTCGATTTGGCAAACCTCAAAG-TTGTTCTTT-AAGTTGTTTATGGCCTAGTTATAATCATT
195 GTCTTCGATTTGGCAAACCTCAAAGCTT-TTCTTTCAA-TTATTTATGGACTAACTACAATCATT
* *
1509 GTGATGATATTAGTCCACTGTGAAGTTCCTAGT-TCATTTGGAACACTTGTTATTTTAAGCCTTT
258 GTGATGAGATTAGTCCACTGTGAAGTTCCTA-TCTCATTTGGAACACTTGTTATTTTAAGCCTAT
** *
1573 CGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCAT
322 CGGGGCCCATTAGTGACGTTTTGAATCGTCTTCGAGTTGGCAAACCTCAATGCTTTTCTTTCCAT
* * * * * *
1638 TGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGTTCATTTG
387 TATATATGGACTAACTATAATCATTTTGGTGAGATTAGTCCACTATGAAGTTTTTAGCTCATTCG
* *
1703 GAACACTTGTTATTTTGGGCCTATCGAGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTCGGC
452 GAACACTTGTTATTTTGGGCCTATCAAGGCCCATTAGTGACGTTTTGAATCGTCTTCAATTCGGC
*
1768 AAACCCTAATGCTTTTCTTTTCATTGTTTCTGGACTAACTATAATCATTTTGG
517 AAACCCTAATGCTTTTCTTTTCATTGTTTATGGACTAACTATAATCATTTTGG
1821 ATTTAGGGCCTATCGGGGCC
1 ATTTAGGGCCTATCGGGGCC
1841 TGATACGAAT
Statistics
Matches: 536, Mismatches: 49, Indels: 9
0.90 0.08 0.02
Matches are distributed among these distances:
569 66 0.12
570 469 0.88
571 1 0.00
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.41
Consensus pattern (569 bp):
ATTTAGGGCCTATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTCGGCAAAACTCAATG
CTTTTCTTTCCATTGTTTATGGACTAACTATAATCATATTGGTGAGATTAGTCCACTGTGAAGTT
TTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTTTTGAATAG
TCTTCGATTTGGCAAACCTCAAAGCTTTTCTTTCAATTATTTATGGACTAACTACAATCATTGTG
ATGAGATTAGTCCACTGTGAAGTTCCTATCTCATTTGGAACACTTGTTATTTTAAGCCTATCGGG
GCCCATTAGTGACGTTTTGAATCGTCTTCGAGTTGGCAAACCTCAATGCTTTTCTTTCCATTATA
TATGGACTAACTATAATCATTTTGGTGAGATTAGTCCACTATGAAGTTTTTAGCTCATTCGGAAC
ACTTGTTATTTTGGGCCTATCAAGGCCCATTAGTGACGTTTTGAATCGTCTTCAATTCGGCAAAC
CCTAATGCTTTTCTTTTCATTGTTTATGGACTAACTATAATCATTTTGG
Found at i:1818 original size:154 final size:154
Alignment explanation
Indices: 1252--1820 Score: 822
Period size: 154 Copynumber: 3.7 Consensus size: 154
1242 ATCATTTTGG
* *
1252 ATTTCGGGCCTATCGAGGCCCATTAGTGACGTTTTGAATCGTCTTTGATTCGGCAAACC-CTAAT
1 ATTTTGGGCCTATCGAGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTCGGCAAACCTC-AAT
* *
1316 GCTTTTCTTTTCATTTTTTATGGACTAACTATAATCATATTGGTGAGATTAGTCCACTGTGAAGT
65 GCTTTTCTTTTCATTGTTTATGGACTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGT
*
1381 TTTTAGCTCATTTGGAACACTTGTT
130 TTTTAGTTCATTTGGAACACTTGTT
* * * *
1406 ATTTTGGGCCTATCGGGGCCCATTAGTGACGTTTTGAATCTTCTTCGATTTGGCAAACCTCAAAG
1 ATTTTGGGCCTATCGAGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTCGGCAAACCTCAATG
* * ** * * *
1471 -TTGTTC-TTTAAGTTGTTTATGGCCTAGTTATAATCATTGTGATGATATTAGTCCACTGTGAAG
66 CTT-TTCTTTTCA-TTGTTTATGGACTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAG
**
1534 TTCCTAGTTCATTTGGAACACTTGTT
129 TTTTTAGTTCATTTGGAACACTTGTT
** * * ** *
1560 ATTTTAAGCCTTTCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATG
1 ATTTTGGGCCTATCGAGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTCGGCAAACCTCAATG
* *
1625 CTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTT
66 CTTTTCTTTTCATTGTTTATGGACTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTT
1690 TTTAGTTCATTTGGAACACTTGTT
131 TTTAGTTCATTTGGAACACTTGTT
1714 ATTTTGGGCCTATCGAGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTCGGCAAACC-CTAAT
1 ATTTTGGGCCTATCGAGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTCGGCAAACCTC-AAT
*
1778 GCTTTTCTTTTCATTGTTTCTGGACTAACTATAATCATTTTGG
65 GCTTTTCTTTTCATTGTTTATGGACTAACTATAATCATTTTGG
1821 ATTTAGGGCC
Statistics
Matches: 365, Mismatches: 44, Indels: 12
0.87 0.10 0.03
Matches are distributed among these distances:
153 7 0.02
154 352 0.96
155 6 0.02
ACGTcount: A:0.22, C:0.18, G:0.19, T:0.41
Consensus pattern (154 bp):
ATTTTGGGCCTATCGAGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTCGGCAAACCTCAATG
CTTTTCTTTTCATTGTTTATGGACTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTT
TTTAGTTCATTTGGAACACTTGTT
Found at i:3047 original size:154 final size:154
Alignment explanation
Indices: 2767--3847 Score: 1772
Period size: 154 Copynumber: 7.0 Consensus size: 154
2757 TGGCGCATCA
*
2767 GGGCCCATTAGTTCCGTTTTGAATCATCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTG
1 GGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTG
* * *
2832 TTTATCGACTAACTATAATCATTGTGATGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGA
66 TTTATGGCCTAACTATAATCATTTTGATGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGA
* *
2897 ACACTTCTTATTTTAGGCCTATCG
131 ACACTTGTTATTTTGGGCCTATCG
2921 GGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTG
1 GGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTG
* *
2986 TTTATGGCCTAACTATAATCATTTTGCTGAGATTAGTCCACTGTGAAGTTTTTAACTCATTTGGA
66 TTTATGGCCTAACTATAATCATTTTGATGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGA
3051 ACACTTGTTATTTTGGGCCTATCG
131 ACACTTGTTATTTTGGGCCTATCG
** *
3075 GGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCAATTG
1 GGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTG
3140 TTTATGGCCTAACTATAATCATTTTGATGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGA
66 TTTATGGCCTAACTATAATCATTTTGATGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGA
* *
3205 ACACTTCTTATTTTGGTCCTATC-
131 ACACTTGTTATTTTGGGCCTATCG
*
3228 GGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACATCAATGCTTTTCTTTCCATTG
1 GGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTG
* * * * *
3293 TTTAGGGACTAACTATAATCATTTTGATGAGATTAGTCCATTGTGAAGTTTTTTGGTCATTTGGA
66 TTTATGGCCTAACTATAATCATTTTGATGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGA
* * *
3358 ACACTTCTTATTTTGGTCCTATCA
131 ACACTTGTTATTTTGGGCCTATCG
* *
3382 GGGCCAATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACGTCAATGCTTTTCTTTCCATTG
1 GGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTG
* * *
3447 TTTATGGACTAACTACAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGA
66 TTTATGGCCTAACTATAATCATTTTGATGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGA
3512 ACACTTGTTATTTTGGGCCTATCG
131 ACACTTGTTATTTTGGGCCTATCG
** *
3536 GGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCATTG
1 GGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTG
* *
3601 TTTATAGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAG-TTTTAGCTCATTTGGA
66 TTTATGGCCTAACTATAATCATTTTGATGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGA
3665 ACACTTGTTATTTTGGGCCTATCG
131 ACACTTGTTATTTTGGGCCTATCG
** * * *
3689 GGGCCCATTAGTGACATTTTGAATCGTCTTCGATTTGAC-AACCTTCAATGCATTTCTTTCCATT
1 GGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACC-TCAATGCTTTTCTTTCCATT
* * *
3753 GTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCTACTGTGAAGATTTTAGCTCATTTGG
65 GTTTATGGCCTAACTATAATCATTTTGATGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGG
3818 AACACTTGTTATTTTGGGCCTATCG
130 AACACTTGTTATTTTGGGCCTATCG
3843 GGGCC
1 GGGCC
3848 AATT
Statistics
Matches: 875, Mismatches: 49, Indels: 6
0.94 0.05 0.01
Matches are distributed among these distances:
152 3 0.00
153 287 0.33
154 585 0.67
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.41
Consensus pattern (154 bp):
GGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTG
TTTATGGCCTAACTATAATCATTTTGATGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGA
ACACTTGTTATTTTGGGCCTATCG
Found at i:3402 original size:307 final size:308
Alignment explanation
Indices: 2763--3847 Score: 1771
Period size: 307 Copynumber: 3.5 Consensus size: 308
2753 TCCTTGGCGC
** *
2763 ATCAGGGCCCATTAGTTCCGTTTTGAATCATCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCC
1 ATCAGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCC
* *
2828 ATTGTTTATCGACTAACTATAATCATTGTGATGAGATTAGTCCACTGTGAAGTTTTTAGCTCATT
66 ATTGTTTATGGACTAACTATAATCATTTTGATGAGATTAGTCCACTGTGAAGTTTTTAGCTCATT
*
2893 TGGAACACTTCTTATTTTAGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTG
131 TGGAACACTTCTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTG
*
2958 GCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGCTGAGATTAGT
196 GCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGATGAGATTAGT
*
3023 CCACTGTGAAGTTTTTAACTCATTTGGAACACTTGTTATTTTGGGCCT
261 CCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCT
* *
3071 ATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCA
1 ATCAGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCC
*
3136 ATTGTTTATGGCCTAACTATAATCATTTTGATGAGATTAGTCCACTGTGAAGTTTTTAGCTCATT
66 ATTGTTTATGGACTAACTATAATCATTTTGATGAGATTAGTCCACTGTGAAGTTTTTAGCTCATT
*
3201 TGGAACACTTCTTATTTTGGTCCTATC-GGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTG
131 TGGAACACTTCTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTG
* * *
3265 GCAAACATCAATGCTTTTCTTTCCATTGTTTAGGGACTAACTATAATCATTTTGATGAGATTAGT
196 GCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGATGAGATTAGT
* * * * *
3330 CCATTGTGAAGTTTTTTGGTCATTTGGAACACTTCTTATTTTGGTCCT
261 CCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCT
* ** *
3378 ATCAGGGCCAATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACGTCAATGCTTTTCTTTCC
1 ATCAGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCC
* *
3443 ATTGTTTATGGACTAACTACAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATT
66 ATTGTTTATGGACTAACTATAATCATTTTGATGAGATTAGTCCACTGTGAAGTTTTTAGCTCATT
* **
3508 TGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTG
131 TGGAACACTTCTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTG
* * *
3573 GCAACCCTCAATGCTTTTCTTTCCATTGTTTATAGCCTAACTATAATCATTTTGGTGAGATTAGT
196 GCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGATGAGATTAGT
3638 CCACTGTGAAG-TTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCT
261 CCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCT
* * * *
3685 ATCGGGGCCCATTAGTGACATTTTGAATCGTCTTCGATTTGAC-AACCTTCAATGCATTTCTTTC
1 ATCAGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACC-TCAATGCTTTTCTTTC
* * * *
3749 CATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCTACTGTGAAGATTTTAGCTCAT
65 CATTGTTTATGGACTAACTATAATCATTTTGATGAGATTAGTCCACTGTGAAGTTTTTAGCTCAT
*
3814 TTGGAACACTTGTTATTTTGGGCCTATCGGGGCC
130 TTGGAACACTTCTTATTTTGGGCCTATCGGGGCC
3848 AATT
Statistics
Matches: 719, Mismatches: 56, Indels: 5
0.92 0.07 0.01
Matches are distributed among these distances:
306 3 0.00
307 465 0.65
308 251 0.35
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.40
Consensus pattern (308 bp):
ATCAGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCC
ATTGTTTATGGACTAACTATAATCATTTTGATGAGATTAGTCCACTGTGAAGTTTTTAGCTCATT
TGGAACACTTCTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTG
GCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGATGAGATTAGT
CCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCT
Found at i:3634 original size:461 final size:460
Alignment explanation
Indices: 2767--3851 Score: 1830
Period size: 461 Copynumber: 2.4 Consensus size: 460
2757 TGGCGCATCA
* *
2767 GGGCCCATTAGTTCCGTTTTGAATCATCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTG
1 GGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACATCAATGCTTTTCTTTCCATTG
* *
2832 TTTATCGACTAACTATAATCATTGTGATGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGA
66 TTTATGGACTAACTATAATCATTTTGATGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGA
*
2897 ACACTTCTTATTTTAGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAA
131 ACACTTCTTATTTT-GGCCTATCGGGGCCAATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAA
* *
2962 ACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGCTGAGATTAGTCCAC
195 ACCTCAATGCTTTTCTTTCCATTGTTTATGGACTAACTACAATCATTTTGCTGAGATTAGTCCAC
3027 TGTGAAGTTTTTAACTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGT
260 TGTGAAGTTTTTAACTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGT
*
3092 TTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCAATTGTTTATGGCCTAACTATA
325 TTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCAATTGTTTATAGCCTAACTATA
*
3157 ATCATTTTGATGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTCTTATTTTGGT
390 ATCATTTTGATGAGATTAGTCCACTGTGAAG-TTTTAGCTCATTTGGAACACTTCTTATTTTGGG
3222 CCTATC-
454 CCTATCG
3228 GGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACATCAATGCTTTTCTTTCCATTG
1 GGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACATCAATGCTTTTCTTTCCATTG
* * * *
3293 TTTAGGGACTAACTATAATCATTTTGATGAGATTAGTCCATTGTGAAGTTTTTTGGTCATTTGGA
66 TTTATGGACTAACTATAATCATTTTGATGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGA
*
3358 ACACTTCTTATTTTGGTCCTATCAGGGCCAATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAA
131 ACACTTCTTATTTTGG-CCTATCGGGGCCAATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAA
* *
3423 ACGTCAATGCTTTTCTTTCCATTGTTTATGGACTAACTACAATCATTTTGGTGAGATTAGTCCAC
195 ACCTCAATGCTTTTCTTTCCATTGTTTATGGACTAACTACAATCATTTTGCTGAGATTAGTCCAC
*
3488 TGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGT
260 TGTGAAGTTTTTAACTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGT
* *
3553 TTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCATTGTTTATAGCCTAACTATA
325 TTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCAATTGTTTATAGCCTAACTATA
* *
3618 ATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTAGCTCATTTGGAACACTTGTTATTTTGGGC
390 ATCATTTTGATGAGATTAGTCCACTGTGAAGTTTTAGCTCATTTGGAACACTTCTTATTTTGGGC
3683 CTATCG
455 CTATCG
** * * * * *
3689 GGGCCCATTAGTGACATTTTGAATCGTCTTCGATTTGACAACCTTCAATGCATTTCTTTCCATTG
1 GGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACATCAATGCTTTTCTTTCCATTG
* * * *
3754 TTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCTACTGTGAAGATTTTAGCTCATTTGGA
66 TTTATGGACTAACTATAATCATTTTGATGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGA
*
3819 ACACTTGTTATTTTGGGCCTATCGGGGCCAATT
131 ACACTTCTTATTTT-GGCCTATCGGGGCCAATT
Statistics
Matches: 583, Mismatches: 38, Indels: 6
0.93 0.06 0.01
Matches are distributed among these distances:
460 39 0.07
461 542 0.93
462 2 0.00
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.41
Consensus pattern (460 bp):
GGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACATCAATGCTTTTCTTTCCATTG
TTTATGGACTAACTATAATCATTTTGATGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGA
ACACTTCTTATTTTGGCCTATCGGGGCCAATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAA
CCTCAATGCTTTTCTTTCCATTGTTTATGGACTAACTACAATCATTTTGCTGAGATTAGTCCACT
GTGAAGTTTTTAACTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTT
TTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCAATTGTTTATAGCCTAACTATAA
TCATTTTGATGAGATTAGTCCACTGTGAAGTTTTAGCTCATTTGGAACACTTCTTATTTTGGGCC
TATCG
Done.