Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_773 ID=scaffold_773-JGI_221_v2.0
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: 3931
ACGTcount: A:0.28, C:0.23, G:0.17, T:0.30
Warning! 100 characters in sequence are not A, C, G, or T
Found at i:238 original size:132 final size:132
Alignment explanation
Indices: 1--904 Score: 1209
Period size: 132 Copynumber: 6.8 Consensus size: 132
* * * * * * *
1 TTAGGGAGATTGGACTAATGGCTTACATCTACTTCTCCACCGTATTTGGAAGGTAAGATTCAGCA
1 TTAGGGAGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCA
* *
66 TCTTCGATCTACTCCACTACTGCTTAGTGTGACAGAATCTGCAATCTTCAACCTACTCAACTACT
66 TCTTCGATCTACTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACT
*
131 AC
131 GC
* * *
133 TTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAAATAAGATTCATCA
1 TTAGGGAGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCA
* * * ** * * * * *
198 TATTCGATCTGCTTCACTACTATTTAAGGTGACAGAATCTGTAATCTTCAATCAATTCCACTA-T
66 TCTTCGATCTACTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACT
262 GGC
131 -GC
* * *
265 TTAGGGAGATAGGGCTAATGGCTAAAATCTGCTTCTCCACTGTATTGGGAAAATAAGATTCACCA
1 TTAGGGAGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCA
* *
330 TCTTCGATCTACTCCAATACTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCTCTACT
66 TCTTCGATCTACTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACT
395 GC
131 GC
* * * * * *
397 TTAGGGAGATTGGACTAATGGCTCAAATCTGCTTCTCCACTATCTTGAGAAGATAAGAATCACCA
1 TTAGGGAGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCA
* *
462 TCTTCAATCCACTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACT
66 TCTTCGATCTACTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACT
527 GC
131 GC
* * * * *
529 TTACGGTGATAGTACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAGGATTGACCA
1 TTAGGGAGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCA
* * *
594 TCGTCGATCTACTCTACTACTGCTTAGGGTGACAGAATCTGCAATCTTTAACCTACTCCACTACT
66 TCTTCGATCTACTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACT
659 GC
131 GC
* * * * * * * *
661 TTTGGGTGATAGCACAAATGGTTTAAATCTGCTTCTCCACTGTATTGGGAAAATAGGATTCATCA
1 TTAGGGAGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCA
* ** * * * *
726 TATTTAATCTGCTTCACTACTGCTTAGGGTGACAGAATCTGCAATCTTCAATCGACTCCACTACT
66 TCTTCGATCTACTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACT
*
791 GG
131 GC
* *
793 TTAGGGAGATTGGACTAATGGCTTAAATATGCTTC-CCTACTGTATTGGGAAGATAAGATTCACC
1 TTAGGGAGATAGGACTAATGGCTTAAATCTGCTTCTCC-ACTGTATTGGGAAGATAAGATTCACC
*
857 ATCTTCGATCTACTCCACTACTGCTTGGGGTGACAGAATCTGCAATCT
65 ATCTTCGATCTACTCCACTACTGCTTAGGGTGACAGAATCTGCAATCT
905 NNNNNNNNNN
Statistics
Matches: 668, Mismatches: 101, Indels: 6
0.86 0.13 0.01
Matches are distributed among these distances:
131 3 0.00
132 664 0.99
133 1 0.00
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.31
Consensus pattern (132 bp):
TTAGGGAGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCA
TCTTCGATCTACTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACT
GC
Found at i:386 original size:44 final size:44
Alignment explanation
Indices: 329--669 Score: 154
Period size: 44 Copynumber: 7.8 Consensus size: 44
319 AAGATTCACC
* * *
329 ATCTTCGATCTACTCCAATACTGCTTAGGGTGACAGAATCTGCA
1 ATCTTCAACCTACTCCACTACTGCTTAGGGTGACAGAATCTGCA
* * ** *
373 ATCTTCAACCTACTCCTCTACTGCTTAGGGAGATTGGA-CT--A
1 ATCTTCAACCTACTCCACTACTGCTTAGGGTGACAGAATCTGCA
* * * *
414 ATGGC-TCAAATCTGCTTCTCCACTA-T-CTTGAGAAGAT-A-AGAATC-ACC
1 AT--CTTC-AA-C--CTACTCCACTACTGCTT-AG--GGTGACAGAATCTGCA
461 ATCTTCAATCC-ACTCCACTACTGCTTAGGGTGACAGAATCTGCA
1 ATCTTCAA-CCTACTCCACTACTGCTTAGGGTGACAGAATCTGCA
* * *
505 ATCTTCAACCTACTCCACTACTGCTTACGGTGATAGTA-CT--A
1 ATCTTCAACCTACTCCACTACTGCTTAGGGTGACAGAATCTGCA
* * * * * * * * * * *
546 ATGGCTTAAATCTGCTTCTCCACTG-TATTGGGAAGATAGGAT-TGACC
1 AT--CTTCAACCTACTCCACTACTGCT-TAGGG-TGACAGAATCTG-CA
* * * *
593 ATCGTCGATCTACTCTACTACTGCTTAGGGTGACAGAATCTGCA
1 ATCTTCAACCTACTCCACTACTGCTTAGGGTGACAGAATCTGCA
* *
637 ATCTTTAACCTACTCCACTACTGCTTTGGGTGA
1 ATCTTCAACCTACTCCACTACTGCTTAGGGTGA
670 TAGCACAAAT
Statistics
Matches: 216, Mismatches: 52, Indels: 58
0.66 0.16 0.18
Matches are distributed among these distances:
41 8 0.04
42 12 0.06
43 37 0.17
44 111 0.51
45 29 0.13
46 14 0.06
47 5 0.02
ACGTcount: A:0.26, C:0.26, G:0.17, T:0.30
Consensus pattern (44 bp):
ATCTTCAACCTACTCCACTACTGCTTAGGGTGACAGAATCTGCA
Found at i:1244 original size:132 final size:132
Alignment explanation
Indices: 1005--3076 Score: 2895
Period size: 132 Copynumber: 15.7 Consensus size: 132
995 NNNNNNNNNN
*
1005 GTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGCATTGGGAAGATAAGATTCACCATCTTC
1 GTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTC
* * *
1070 GATCTGCAT-CACTACTAG-TTAGGGTGACAGAATCTGTAATCTTCAACCAATTCCACTA-TGGC
66 GATCTGC-TCCACTACT-GCTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACT-GC
1132 TTAGG
128 TTAGG
* * * * ** * *
1137 GAGATAGAACTAATGGCTTAAATCTACTTTTCCACTGTATTGAAAAAATAACATTCACCATCTTC
1 GTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTC
* * * * * *
1202 GATCTACTCCACTACAGCTTAGGATGACAGAGTCTGCAATCTTCAGCCTATTCCACTACTGCTTA
66 GATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTA
1267 GG
131 GG
* * * *
1269 GTGATAGGACTAATGGCTTAAAACTGCTTCTCCACTATATTGGGAAGATAACATTCACCATATTC
1 GTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTC
1334 GATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTA
66 GATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTA
1399 GG
131 GG
* * * *
1401 GTGATTGGACTAATGGCTTAAATCTGCTTCTCCACTATATTGGGAAGATAAGATTCATCATATTC
1 GTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTC
* * * * * * *
1466 GATCTGCTCCACTACGGCTTAGGTTGACAAAATCTGGAATCTTCAACCAATTCCAC-AATGGCTT
66 GATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACT-GCTT
1530 AGG
130 AGG
* * *
1533 GAGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGTGAAAATAAGATTCACCATCTTC
1 GTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTC
** *
1598 GATCTATTCCAAC-ACTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTACTT
66 GATCTGCTCC-ACTACTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTT
1662 AGG
130 AGG
* * * *
1665 GTGATAGGACTAATGGCATAAATCTACTTCTCCACTGTATTGGGAA-AGTAAGATTCATCATATT
1 GTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGA-TAAGATTCACCATCTT
* * * * *
1729 CGATCTGTTTCACTACTGTTTAGGGTGACAGAATCTGCAATCTTCAACCAATTCCACTA-TGGCT
65 CGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACT-GCT
1793 TAGG
129 TAGG
* * * * * *
1797 GAGATAGAACAAATGGCTTAAATCTACTTCTCCACTGTATTGGGAAAATAAGATTCACCAACTTC
1 GTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTC
* *
1862 GATCTACTCCACTACAGCTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTA
66 GATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTA
*
1927 AG
131 GG
* *
1929 GTGATAGGACTAATGGCTTAAATATGCATGCTTCTCCACTATATTGGAAAGATAAGATTCACCAT
1 GTGATAGGACTAATGGCTT-AA-AT-C-TGCTTCTCCACTGTATTGGGAAGATAAGATTCACCAT
* * * *
1994 ATTCGATCTGCTGCACTACTGCTTAGGGTGACAGAATCTGGAATCTTCAACCAACTCCACTACTG
62 CTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTG
2059 CTTAGG
127 CTTAGG
* *
2065 GTGATATGACTAATGGCTTAAATCTGCTTCTCTACTGTATTGGGAAGATAAGATTCACCATCTTC
1 GTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTC
** * * *
2130 GATCTGCTCCACTACTGCTTATAGTGACAGAATTTGCAATCTTCAACCAACTCCAGTACTGCTTA
66 GATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTA
2195 GG
131 GG
* * *
2197 GTGATAGGACTAATGGCTTAAATCTCCTTCTCCACTGTATTGGGAAGATAAGATTGACCATATTC
1 GTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTC
* *
2262 GATCAGCTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTCCTTA
66 GATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTA
2327 GG
131 GG
* * *
2329 GTGATAGGACTAATGGCTTAAATCTGCTTCTCCACAGTATTGGGAAGATAGGATTCACCATCGTC
1 GTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTC
* *
2394 GATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTTAACCTACACCACTACTGCTTA
66 GATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTA
2459 GG
131 GG
* * * * *
2461 GCGATATGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAAATAAGATTCATCATATTC
1 GTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTC
* * * *
2526 GATCTGCTTCACTACTG-TTAAGGGTGACAGAATCTGTAATCTTCAACCAATTCCACTA-TGGCT
66 GATCTGCTCCACTACTGCTT-AGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACT-GCT
2589 TAGG
129 TAGG
* * * *
2593 GAGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTTGAAAAATAAGATTCACCATCTTC
1 GTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTC
** * * *
2658 GATCTATTCCAATACTGCTTACGGTGAGAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTA
66 GATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTA
2723 GG
131 GG
* * * * * * *
2725 GAGATTGGACTAATGGCTGAAATCTGCTTCTCCACTTTCTTGAGAAGATAAGAATCACCATCTTC
1 GTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTC
* * *
2790 GATCCGCTACACTACTGCTTAAGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTA
66 GATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTA
2855 GG
131 GG
* * *
2857 GTGATAGGACTAATGGCTTAAATCCGCTTCTCCACCGTATTGCGAAGATAAGATTCACCATCTTC
1 GTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTC
* *
2922 GATCTGCAT-CACTACTGCTTAGGGTGACAGAATCTACAATCTTCAACCGACTCCACTACTGCTT
66 GATCTGC-TCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTT
2986 AGG
130 AGG
* * *
2989 GTGATAGGACTAATGGCTTAAATGTGCTTCTCCACTGTATTGGGAAGATAGGATTCACCATCGTC
1 GTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTC
*
3054 GATCTGCTCCACTACTTCTTAGG
66 GATCTGCTCCACTACTGCTTAGG
3077 TAGATTAGAC
Statistics
Matches: 1719, Mismatches: 200, Indels: 42
0.88 0.10 0.02
Matches are distributed among these distances:
131 12 0.01
132 1572 0.91
133 14 0.01
134 4 0.00
135 3 0.00
136 114 0.07
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.30
Consensus pattern (132 bp):
GTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTC
GATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTA
GG
Found at i:3121 original size:88 final size:87
Alignment explanation
Indices: 2971--3164 Score: 309
Period size: 88 Copynumber: 2.2 Consensus size: 87
2961 TCTTCAACCG
*
2971 ACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATGTGCTTCTCCACTGTATTGGGAAG
1 ACTCCACTACTGCTTA-GGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAG
*
3036 ATAGGATTCACCATCGTCGATCT
65 ATAAGATTCACCATCGTCGATCT
* *
3059 GCTCCACTACTTCTTAGGTAGATTA-GACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAA
1 ACTCCACTACTGCTTAGGT-GA-TAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAA
*
3123 GATAAGATTCACCATCTTCGATCT
64 GATAAGATTCACCATCGTCGATCT
3147 ACTCCACTACTGCTTAGG
1 ACTCCACTACTGCTTAGG
3165 GTGACTGAAT
Statistics
Matches: 97, Mismatches: 7, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
87 3 0.03
88 92 0.95
89 2 0.02
ACGTcount: A:0.25, C:0.23, G:0.20, T:0.32
Consensus pattern (87 bp):
ACTCCACTACTGCTTAGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGA
TAAGATTCACCATCGTCGATCT
Found at i:3126 original size:220 final size:220
Alignment explanation
Indices: 2840--3300 Score: 696
Period size: 220 Copynumber: 2.1 Consensus size: 220
2830 CTTCAACCTA
2840 CTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCCGCTTCTCCACCGTATTGCGAAGA
1 CTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCCGCTTCTCCACCGTATTGCGAAGA
*
2905 TAAGATTCACCATCTTCGATCTGCAT-CACTACTGCTTAGGGTGACAGAATCTACAATCTTCAAC
66 TAAGATTCACCATCTTCGATCTAC-TCCACTACTGCTTAGGGTGACAGAATCTACAATCTTCAAC
* * *
2969 CGACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATGTGCTTCTCCACTGTATTGGG-
130 CGACTCCACTACTACTTAGGGTGATAAGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGA
* *
3033 AAGATAGGATTCACCATCGTCGATCTG
195 AAG-TAAGATTCACCATAGTCGATCTG
* * * *
3060 CTCCACTACTTCTTA-GGTAGATTA-GACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAA
1 CTCCACTACTGCTTAGGGT-GA-TAGGACTAATGGCTTAAATCCGCTTCTCCACCGTATTGCGAA
* *
3123 GATAAGATTCACCATCTTCGATCTACTCCACTACTGCTTAGGGTGACTGAATCTGCAATCTTCAA
64 GATAAGATTCACCATCTTCGATCTACTCCACTACTGCTTAGGGTGACAGAATCTACAATCTTCAA
*
3188 CCTACTCCACTACTACTTAGGGTGATAAGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGG
129 CCGACTCCACTACTACTTAGGGTGATAAGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGG
* *
3253 AAAGTAAGATTCATCATATTCGATCTG
194 AAAGTAAGATTCACCATAGTCGATCTG
* * *
3280 CTTCACTACTGTTTACGGTGA
1 CTCCACTACTGCTTAGGGTGA
3301 CAGAATCTGC
Statistics
Matches: 218, Mismatches: 18, Indels: 10
0.89 0.07 0.04
Matches are distributed among these distances:
219 4 0.02
220 206 0.94
221 8 0.04
ACGTcount: A:0.26, C:0.24, G:0.19, T:0.31
Consensus pattern (220 bp):
CTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCCGCTTCTCCACCGTATTGCGAAGA
TAAGATTCACCATCTTCGATCTACTCCACTACTGCTTAGGGTGACAGAATCTACAATCTTCAACC
GACTCCACTACTACTTAGGGTGATAAGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAA
AGTAAGATTCACCATAGTCGATCTG
Found at i:3300 original size:132 final size:132
Alignment explanation
Indices: 3060--3931 Score: 1015
Period size: 132 Copynumber: 6.6 Consensus size: 132
3050 CGTCGATCTG
* * *
3060 CTCCACTACTTCTTA-GGTAGATTAGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAG
1 CTCCACTACTGCTTAGGGT-GATAAGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAA
* * *
3124 ATAAGATTCACCATCTTCGATCTACTCCACTACTGCTTAGGGTGACTGAATCTGCAATCTTCAAC
65 ATAAGATTCACCATCTTCGATCTGCTTCACTACTGCTTAGGGTGACAGAATCTGCAATCTTCAAC
3189 CTA
130 CTA
* *
3192 CTCCACTACTACTTAGGGTGATAAGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAAG
1 CTCCACTACTGCTTAGGGTGATAAGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAAA
* * * *
3257 TAAGATTCATCATATTCGATCTGCTTCACTACTGTTTACGGTGACAGAATCTGCAATCTTCAACC
66 TAAGATTCACCATCTTCGATCTGCTTCACTACTGCTTAGGGTGACAGAATCTGCAATCTTCAACC
*
3322 AA
131 TA
* * * *
3324 TTCCACTA-TGGCTTAAGGTGAT-AGAACAAATAGCTTAAATCTGCTTCTCCACTGTATTGGGAA
1 CTCCACTACT-GCTTAGGGTGATAAG-ACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAA
* * * * * *
3387 AATAAGATTCACCATCTTCGATCT-ATTCCAATACTACTTAGTGTGACAGAATCAGCAATATTCA
64 AATAAGATTCACCATCTTCGATCTGCTT-CACTACTGCTTAGGGTGACAGAATCTGCAATCTTCA
3451 ACCTA
128 ACCTA
* * ** * * * * *
3456 CTCCACTACTGCTTATGGAGATTGGACTAATGGCTGAAATCTGCTTCTCCACTATCTTGAGAAGA
1 CTCCACTACTGCTTAGGGTGATAAGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAAA
* * **
3521 TAAGAATCACCATCTTCGATCCGC-TCAACTACTGCTTAGGGTGACAGAATCTGCAATCTAAAAC
66 TAAGATTCACCATCTTCGATCTGCTTC-ACTACTGCTTAGGGTGACAGAATCTGCAATCTTCAAC
3585 CTA
130 CTA
*
3588 CTCCACTACTGCTTAGGGTGATATGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAAA
1 CTCCACTACTGCTTAGGGTGATAAGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAAA
** * * * * *
3653 TAAGATTCATTATATTCAATCTGCTTCACTACTGTTTAGGGTGACCGAATCTGTAATCTTCAACC
66 TAAGATTCACCATCTTCGATCTGCTTCACTACTGCTTAGGGTGACAGAATCTGCAATCTTCAACC
*
3718 AA
131 TA
* * *
3720 TTCCACTA-TGGCTTAGGGAGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAA
1 CTCCACTACT-GCTTAGGGTGATAAGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAA
* * * *
3784 ATAAGATTCACCATCTTCGATCTACTCCAAC-ACTGCTTAGGCTGACAGAATTCTACAATCTTCA
65 ATAAGATTCACCATCTTCGATCTGCTTC-ACTACTGCTTAGGGTGACAGAA-TCTGCAATCTTCA
3848 ACCTA
128 ACCTA
* * ** * * * * * * *
3853 CTGCTCTACTGCTTAGGAAGAT-TGACTAATGGCTGAAATATGGC-TCTCCACTATCTTGAGAAG
1 CTCCACTACTGCTTAGGGTGATAAGACTAATGGCTTAAATCT-GCTTCTCCACTGTATTGGGAAA
* *
3916 ATAAGAATGACCATCT
65 ATAAGATTCACCATCT
Statistics
Matches: 627, Mismatches: 99, Indels: 28
0.83 0.13 0.04
Matches are distributed among these distances:
131 7 0.01
132 577 0.92
133 42 0.07
134 1 0.00
ACGTcount: A:0.29, C:0.23, G:0.17, T:0.31
Consensus pattern (132 bp):
CTCCACTACTGCTTAGGGTGATAAGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAAA
TAAGATTCACCATCTTCGATCTGCTTCACTACTGCTTAGGGTGACAGAATCTGCAATCTTCAACC
TA
Found at i:3594 original size:396 final size:396
Alignment explanation
Indices: 3060--3931 Score: 1349
Period size: 396 Copynumber: 2.2 Consensus size: 396
3050 CGTCGATCTG
* * * * * *
3060 CTCCACTACTTCTTAGGTAGATTAGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGA
1 CTCCACTACTGCTTAGGAAGATT-GACTAATGGCTGAAATCTGCTTCTCCACTATCTTGAGAAGA
* * * * **
3125 TAAGATTCACCATCTTCGATCTACTCCACTACTGCTTAGGGTGACTGAATCTGCAATCTTCAACC
65 TAAGAATCACCATCTTCGATCCACTCAACTACTGCTTAGGGTGACAGAATCTGCAATCTAAAACC
3190 TACTCCACTACTACTTAGGGTGATAAGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAA
130 TACTCCACTACTACTTAGGGTGATAAGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAA
* *
3255 AGTAAGATTCATCATATTCGATCTGCTTCACTACTGTTTACGGTGACAGAATCTGCAATCTTCAA
195 AATAAGATTCATCATATTCAATCTGCTTCACTACTGTTTACGGTGACAGAATCTGCAATCTTCAA
*
3320 CCAATTCCACTATGGCTTAAGGTGATAGAACAAATAGCTTAAATCTGCTTCTCCACTGTATTGGG
260 CCAATTCCACTATGGCTTAAGGAGATAGAACAAATAGCTTAAATCTGCTTCTCCACTGTATTGGG
* *
3385 AAAATAAGATTCACCATCTTCGATCTATTCCAATACTACTTAGTG-TGACAGAA-TC-AGCAATA
325 AAAATAAGATTCACCATCTTCGATCTACTCCAACACTACTTAG-GCTGACAGAATTCTA-CAATA
3447 TTCAACCTA
388 TTCAACCTA
3456 CTCCACTACTGCTTATGG-AGATTGGACTAATGGCTGAAATCTGCTTCTCCACTATCTTGAGAAG
1 CTCCACTACTGCTTA-GGAAGATT-GACTAATGGCTGAAATCTGCTTCTCCACTATCTTGAGAAG
*
3520 ATAAGAATCACCATCTTCGATCCGCTCAACTACTGCTTAGGGTGACAGAATCTGCAATCTAAAAC
64 ATAAGAATCACCATCTTCGATCCACTCAACTACTGCTTAGGGTGACAGAATCTGCAATCTAAAAC
* *
3585 CTACTCCACTACTGCTTAGGGTGATATGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGA
129 CTACTCCACTACTACTTAGGGTGATAAGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGA
* * * *
3650 AAATAAGATTCATTATATTCAATCTGCTTCACTACTGTTTAGGGTGACCGAATCTGTAATCTTCA
194 AAATAAGATTCATCATATTCAATCTGCTTCACTACTGTTTACGGTGACAGAATCTGCAATCTTCA
* * * *
3715 ACCAATTCCACTATGGCTTAGGGAGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGG
259 ACCAATTCCACTATGGCTTAAGGAGATAGAACAAATAGCTTAAATCTGCTTCTCCACTGTATTGG
* *
3780 GAAAATAAGATTCACCATCTTCGATCTACTCCAACACTGCTTAGGCTGACAGAATTCTACAATCT
324 GAAAATAAGATTCACCATCTTCGATCTACTCCAACACTACTTAGGCTGACAGAATTCTACAATAT
3845 TCAACCTA
389 TCAACCTA
* * *
3853 CTGCTCTACTGCTTAGGAAGATTGACTAATGGCTGAAATATGGC-TCTCCACTATCTTGAGAAGA
1 CTCCACTACTGCTTAGGAAGATTGACTAATGGCTGAAATCT-GCTTCTCCACTATCTTGAGAAGA
*
3917 TAAGAATGACCATCT
65 TAAGAATCACCATCT
Statistics
Matches: 436, Mismatches: 34, Indels: 12
0.90 0.07 0.02
Matches are distributed among these distances:
395 1 0.00
396 397 0.91
397 37 0.08
398 1 0.00
ACGTcount: A:0.29, C:0.23, G:0.17, T:0.31
Consensus pattern (396 bp):
CTCCACTACTGCTTAGGAAGATTGACTAATGGCTGAAATCTGCTTCTCCACTATCTTGAGAAGAT
AAGAATCACCATCTTCGATCCACTCAACTACTGCTTAGGGTGACAGAATCTGCAATCTAAAACCT
ACTCCACTACTACTTAGGGTGATAAGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAA
ATAAGATTCATCATATTCAATCTGCTTCACTACTGTTTACGGTGACAGAATCTGCAATCTTCAAC
CAATTCCACTATGGCTTAAGGAGATAGAACAAATAGCTTAAATCTGCTTCTCCACTGTATTGGGA
AAATAAGATTCACCATCTTCGATCTACTCCAACACTACTTAGGCTGACAGAATTCTACAATATTC
AACCTA
Done.