Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold861
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: 45654
ACGTcount: A:0.05, C:0.04, G:0.03, T:0.05
Warning! 38055 characters in sequence are not A, C, G, or T
Found at i:243 original size:132 final size:132
Alignment explanation
Indices: 1--1047 Score: 1378
Period size: 132 Copynumber: 7.9 Consensus size: 132
* * * * *
1 CAATCTTCAACCGACTCCACTACTGCTTAGGGAGATTGGACCAATGCCTTAAATCTTCTTCTCCA
1 CAATCTTCAACCTACTCCACTACTGCTTAGGGAGATAGGACTAATGGCTTAAATCTGCTTCTCCA
* * * * *
66 CTGTATTTGGAAGATAAGATTCACCATGTTCGATCTACTCTACTACTGCTTAGGGTGACAGAATC
66 CTGTATTGGGAAAATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATC
131 TG
131 TG
* * * *
133 CAATCTTCAACCTACTCCACTTCTACTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCACCA
1 CAATCTTCAACCTACTCCACTACTGCTTAGGGAGATAGGACTAATGGCTTAAATCTGCTTCTCCA
* * * * * *
198 CTGTATTGGGAAAATAAGATTCATCATATTCGATCTGCTTCACTACTGTTTAGGGTAACAGTATC
66 CTGTATTGGGAAAATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATC
263 TG
131 TG
*
265 CAATCTTCAACCAACTCCACTA-TGGCTTAGGGAGATAGGACTAATGGCTTAAATCTGCTTCTCC
1 CAATCTTCAACCTACTCCACTACT-GCTTAGGGAGATAGGACTAATGGCTTAAATCTGCTTCTCC
* * ** * * * *
329 ACTGTATTGGGAAGATAAGGTTCATAATATTCGACCTACTCCACTACTGCTTAGGGTGACAAAAT
65 ACTGTATTGGGAAAATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAAT
394 CTG
130 CTG
* * * * * *
397 CTATCTTTAACCTACTCCACTACTGCTTAGGGAGATAGGACTAATTGCTTGAATCTACTACTCCA
1 CAATCTTCAACCTACTCCACTACTGCTTAGGGAGATAGGACTAATGGCTTAAATCTGCTTCTCCA
* * *
462 CTGTATTGGGAAAATAAGATTCACTATCTTCGATCTACTCCACTACTGCTTAAGGTGACAGAATC
66 CTGTATTGGGAAAATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATC
527 TG
131 TG
* * * *
529 CAATCTTTAACCTACACCACTACTGCTTAGGGTGATATGACTAATGGCTTAAATCTGCTTCTCCA
1 CAATCTTCAACCTACTCCACTACTGCTTAGGGAGATAGGACTAATGGCTTAAATCTGCTTCTCCA
* * * * * * *
594 CTGTATTAGGAAAACAAGATTCATCATATTCGATCTGCTTCACTGCTGTTTAGGGTGACAGAATC
66 CTGTATTGGGAAAATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATC
659 TG
131 TG
* * * * *
661 TAATCTTCAACCAATTCCACTA-TGGCTTAGGGAGATAGGACAAATGGATTAAATCTGCTTCTCC
1 CAATCTTCAACCTACTCCACTACT-GCTTAGGGAGATAGGACTAATGGCTTAAATCTGCTTCTCC
* ** *
725 ACTGTATTGGGAAAATAAGATTCACCATCTTCGGTCTATTCCAATACTGCTTAGGGTGACAGAAT
65 ACTGTATTGGGAAAATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAAT
790 CTG
130 CTG
* * * *
793 CAATCTTCAACCGACTCCACTACTGCCTAGGGAGATTGGACTAATGGCTTAAATCTACTTCTCCA
1 CAATCTTCAACCTACTCCACTACTGCTTAGGGAGATAGGACTAATGGCTTAAATCTGCTTCTCCA
* * * * * *
858 CTGTATTGGTAAGATAGGATTCACCGTCGTCGATCTGCTCCTCTACTGCTTAGGGTGACAGAATC
66 CTGTATTGGGAAAATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATC
923 TG
131 TG
* *
925 CAATCTTCAACCTACTCCACTACTGCTTAGGGAGATTGGACTAATGGCTCAAATCTGCTTCTCCA
1 CAATCTTCAACCTACTCCACTACTGCTTAGGGAGATAGGACTAATGGCTTAAATCTGCTTCTCCA
* * * * * *
990 CTATCTTGAGAAGATAAGAATCACCATCTTCGATCCGCTCCACTACTGCTTAGGGTGA
66 CTGTATTGGGAAAATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGA
1048 NNNNNNNNNN
Statistics
Matches: 792, Mismatches: 119, Indels: 8
0.86 0.13 0.01
Matches are distributed among these distances:
131 2 0.00
132 788 0.99
133 2 0.00
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.31
Consensus pattern (132 bp):
CAATCTTCAACCTACTCCACTACTGCTTAGGGAGATAGGACTAATGGCTTAAATCTGCTTCTCCA
CTGTATTGGGAAAATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATC
TG
Found at i:2300 original size:132 final size:132
Alignment explanation
Indices: 2063--3625 Score: 1199
Period size: 132 Copynumber: 11.9 Consensus size: 132
2053 NNNNNNNNNN
* * *
2063 GGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTTGGAAGATAAGATTCACCA-CT
1 GGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAAATAAGATTCATCATC-
* *
2127 TTCGATCTACTCCACTACTGCTTAGGATGACAAAATCTGCAATCTTCAACCTACTCCACTACTAC
65 TTCGATCTACTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTAC
2192 TTA
130 TTA
* *
2195 GGGTGATAGGACTAATGGCTTAAATCTGCTTCACCACTGTATTGGGAAAATAAGATTCATCATAT
1 GGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAAATAAGATTCATCATCT
* * * * * * *
2260 TCGATCTGCTTCACTACTGTTTAGGGTGACAGAATCTGCAATCTTCAACCAATTCCAATA-TGGC
66 TCGATCTACTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACT-AC
2324 TTA
130 TTA
** * * * *
2327 GGGACATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTACTGGGAAGATAAGGTTCATCATAT
1 GGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAAATAAGATTCATCATCT
* * * * * *
2392 TCGACCTACTCCACTACTGCTTAGGGTGAGAAAATCTGCTATCTTTAACCTACTCCACTACTGCT
66 TCGATCTACTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTACT
2457 TA
131 TA
* * * * * *
2459 GGGAGATAGGATTAATGGCTTTAATCTACTACTCCACTGTACT-GGAAAGATAAGATTC-TCCAT
1 GGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAA-ATAAGATTCAT-CAT
* * * * *
2522 CTTCGATCTACTCTACTACTGCTTAGGGTGATAGAATCTACAATCTTCAGCCTACTCCACTACCA
64 CTTCGATCTACTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTA
2587 CTTA
129 CTTA
* *
2591 GGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGCATTGGGAAAATAAGATTCACCATCT
1 GGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAAATAAGATTCATCATCT
* * * * *
2656 TCCATCTACTCCACTACTGCTTAGGGTGATAGAATCTACAATCTTCAGCCTACTCCACTACCACT
66 TCGATCTACTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTACT
2721 TA
131 TA
* * ******************
2723 GGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTATCTT----TCNNNNNNNNNNNNNNNN
1 GGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAAATAAGATTCATCATCT
*****************************************************************
2784 NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
66 TCGATCTACTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTACT
**
2849 NN
131 TA
***** * * * *
2851 NNNNNATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTACTGGGAAGATAAGGTTCATCATAT
1 GGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAAATAAGATTCATCATCT
* * * * * *
2916 TCGACCTACTCCACTACTGCTTAGGGTGAGAAAATCTGCTATCTTTAACCTACTCCACTACTGCT
66 TCGATCTACTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTACT
2981 TA
131 TA
* * * * * *
2983 GGGAGATAGGATTAATGGCTTTAATCTACTACTCCACTGTACT-GGAAAGATAAGATTC-TCCAT
1 GGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAA-ATAAGATTCAT-CAT
* * *
3046 CTTCGATCTACTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTTAACCTACACCACTACTG
64 CTTCGATCTACTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTA
3111 CTTA
129 CTTA
* * *
3115 GGGTGATATGACTAATGGCTTAAATCTGCTTCTCCACTGTATTAGGAAAATCAA-ATTCATCATA
1 GGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAAAT-AAGATTCATCATC
* * * * * * * * **
3179 TTCGATTTGCTTCACTACTGTTTAGGGTGACAGAATCTGTAATCGTCAACCAATTCCACTACGGC
65 TTCGATCTACTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTAC
3244 TTA
130 TTA
* * * * *
3247 GGGAGATAGGACTAATGGCTTAAATATGCTTCTCCACTGTATTGGGAAGATAAGATGCACCATCT
1 GGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAAATAAGATTCATCATCT
*
3312 TCGATC-AGCTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCTCTAC-AG
66 TCGATCTA-CTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTA-
3375 CTTA
129 CTTA
* * * * * * * * * * *
3379 TGGAGATTGGACTAATGGCTCAAATCTGCTTCTCCATTATCTTGAGAAGATAAGAATCACCATCT
1 GGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAAATAAGATTCATCATCT
** **
3444 TCGATCCGCTCCACTACTGCTTAGGGTGACAGAATCTAAAATCTTCAACCTACTCCACTACTACT
66 TCGATCTACTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTACT
3509 TA
131 TA
* *
3511 GGGTGATAGGACTAATGGCTTAAATCAGCTTCTCCACTGTATTGGGAAAATAAGATTCACCATCT
1 GGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAAATAAGATTCATCATCT
* * * *
3576 TTGATCTACTTCAATACTGCATAGGGTGACAGAATCTGCAATCTTCAACC
66 TCGATCTACTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTCAACC
3626 GANNNNNNNN
Statistics
Matches: 1083, Mismatches: 327, Indels: 42
0.75 0.23 0.03
Matches are distributed among these distances:
128 35 0.03
131 13 0.01
132 1020 0.94
133 15 0.01
ACGTcount: A:0.27, C:0.22, G:0.16, T:0.29
Consensus pattern (132 bp):
GGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAAATAAGATTCATCATCT
TCGATCTACTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTACT
TA
Found at i:2577 original size:44 final size:44
Alignment explanation
Indices: 2529--2731 Score: 148
Period size: 44 Copynumber: 4.6 Consensus size: 44
2519 CATCTTCGAT
*
2529 CTACTCTACTACTGCTTAGGGTGATAGAATCTACAATCTTCAGC
1 CTACTCCACTACTGCTTAGGGTGATAGAATCTACAATCTTCAGC
** * * **
2573 CTACTCCACTACCACTTAGGGTGATAGGA-CT--AATGGCTTAAAT
1 CTACTCCACTACTGCTTAGGGTGATAGAATCTACAAT--CTTCAGC
* * * * ** * * *
2616 CTGCTTCTCCACTGCATT-GGGAAAATAAGATTC-ACCATCTTCCA-T
1 CTACTCCACTACTGC-TTAGGG-TGAT-AGAATCTACAATCTT-CAGC
2661 CTACTCCACTACTGCTTAGGGTGATAGAATCTACAATCTTCAGC
1 CTACTCCACTACTGCTTAGGGTGATAGAATCTACAATCTTCAGC
**
2705 CTACTCCACTACCACTTAGGGTGATAG
1 CTACTCCACTACTGCTTAGGGTGATAG
2732 GACTAATGGC
Statistics
Matches: 117, Mismatches: 30, Indels: 24
0.68 0.18 0.14
Matches are distributed among these distances:
41 3 0.03
43 25 0.21
44 65 0.56
45 20 0.17
46 2 0.02
47 2 0.02
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.30
Consensus pattern (44 bp):
CTACTCCACTACTGCTTAGGGTGATAGAATCTACAATCTTCAGC
Found at i:40816 original size:132 final size:132
Alignment explanation
Indices: 40577--44330 Score: 4812
Period size: 132 Copynumber: 28.6 Consensus size: 132
40567 NNNNNNNNNN
* * * *
40577 TTAAATCTGCTTCTCCACTGTATTTGGATGATAAGATTCACAATCTTTGATCT--ATTCCAAC-A
1 TTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCA-T-C-ACTA
* * * *
40639 CTGCTTAGGGTGATAGAATCTGCAATCCTCAACCTACTCAACTACTGCTTAGGGAGATTGGACTA
63 CTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGATTGGACTA
40704 ATGGC
128 ATGGC
* * * * * * *
40709 TGAAATCTGCTTCTCCACTGTCTTGAGAAGAAAAGAATCCCCATCTTCGATCCGC-TCCACTACT
1 TTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCAT-CACTACT
* * * * * **
40773 GCTAAGGGGGACAGAATCTGCAATCTTTAACCTATTCCACTACTTCTTAGGGTGATAAGACTAAT
65 GCTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGATTGGACTAAT
*
40838 GGA
130 GGC
*
40841 TTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATATTCGATCTGCATCACTACTG
1 TTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCATCACTACTG
* * * * * *
40906 GTTAGTGTGACAGAATCTGTAATCTACAACCTACTCCACTACTGCTTATGGTGATTGGACTAACG
66 CTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGATTGGACTAATG
40971 GC
131 GC
*
40973 TTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATATTCGATCTGCATCACTACTG
1 TTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCATCACTACTG
* * * * * *
41038 GTTAGTGTGACAGAATCTGTAATCTACAACCTACTCCACTACTGCTTATGGTGATTGGACTAACG
66 CTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGATTGGACTAATG
41103 GC
131 GC
*
41105 TTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATATTCGATCTGCATCACTACTG
1 TTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCATCACTACTG
* * * * * *
41170 GTTAGTGTGACAGAATCTGTAATCTACAACCTACTCCACTACTGCTTATGGTGATTGGACTAACG
66 CTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGATTGGACTAATG
41235 GC
131 GC
*
41237 TTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATATTCGATCTGCATCACTACTG
1 TTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCATCACTACTG
* * * * * *
41302 GTTAGTGTGACAGAATCTGTAATCTACAACCTACTCCACTACTGCTTATGGTGATTGGACTAACG
66 CTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGATTGGACTAATG
41367 GC
131 GC
* *
41369 TTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCCTCTTCGATCTTC-TCCACTACT
1 TTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCAT-CACTACT
* * * * *
41433 GCTTAGGGCGACAGAATCTGCAATCTTTAACCTGCACCACTACTGCTTAAGGTGATAT-GACTAA
65 GCTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGAT-TGGACTAA
41497 TGGC
129 TGGC
* * * * * * *
41501 TTAAATTTCCTTCTCCACTGTATTGGGAAAATAAGATTCATCATATTCGATCTGCTTCGCTACTG
1 TTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCATCACTACTG
* * * * * *
41566 TTTAGGGTGACAGAATCTGTAATCTTCAACCAATTCCACTA-TGGCTTAGGGAGATAGGACTAAT
66 CTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACT-GCTTAGGGTGATTGGACTAAT
41630 GGC
130 GGC
* ***
41633 TTAAATCTGCTTCTCCACTGTATTGGGAAAATAAGATTCACNNNC-T--A-CTG---------T-
1 TTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCATCACTACTG
*
41684 -TTAGGGTGACAGAATCTGTAATCTTTCAA-CTAACTCCACTAC-GCTTAGGGTGATTGGACTAA
66 CTTAGGGTGACAGAATCTGCAATC-TTCAACCT-ACTCCACTACTGCTTAGGGTGATTGGACTAA
41746 TGGC
129 TGGC
* * * * *
41750 TTAAATCTGCTTCTCCACTGTATTGGGAA-AGTAAGATTCATCATATTTCGATTTGCTTCCCTAC
1 TTAAATCTGCTTCTCCACTGTATTGGGAAGA-TAAGATTCACCAT-CTTCGATCTGCATCACTAC
** * * * * *
41814 TTTTTAGGGTGACAGAATCTGCAATCTTCAACC-AATTCACTA-TAGCTTAGGGAGATAGGACAA
64 TGCTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACT-GCTTAGGGTGATTGGACTA
*
41877 ATGGA
128 ATGGC
* * * *
41882 TTAAATCTGCTTTTCCACTGTATTGGGAAAATAAGATTCACCACCTTCGATCTAC-TCCACTACA
1 TTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCAT-CACTAC-
* * *
41946 T-CTTAGGGTGACAGAATCTGCAATCTTCAGCCTACTCCACTACTACTTAGGGAGATTGGACTAA
64 TGCTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGATTGGACTAA
42010 TGGC
129 TGGC
* * * * * * * * *
42014 TGAAATCTGCTTCTCCAATATCTTGAGAAGATAAGAATCCCCATCGTCGATCCGC-TCCACTACT
1 TTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCAT-CACTACT
* * * * * * **
42078 GCGTAGGGGGACTGAATCTGCAATCTTTAACCTACTCCACTACTTCTTAGTGTGATAAGACTAAT
65 GCTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGATTGGACTAAT
*
42143 GGA
130 GGC
* * * *
42146 TTAAATCTGCATCTCCACTATCTTGGGAAGATAAGATTCACCATCTTCGATCTGCATCACTACAG
1 TTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCATCACTACTG
* * *
42211 GTTAGGGTGACAGAATCTGCAATCTACAACCTACTCCACCACTGCTTAGGGTGATTGGACTAATG
66 CTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGATTGGACTAATG
42276 GC
131 GC
* * *
42278 TTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTTACCATCTTCGATTTAC-TCCACTACT
1 TTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCAT-CACTACT
** * * * *
42342 GCTTAGGGTGACAGAATCTATAATCTTTAACCTACTCCACTAGTACTTAGGGTGATAGGACTAAT
65 GCTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGATTGGACTAAT
42407 GGC
130 GGC
*
42410 TTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCATCACTACAG
1 TTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCATCACTACTG
* * * *
42475 GTTAGGGTGACAGAATCTGCAATCTACACCCTACTCCACCACTGCTTAGGGTGATTGGACTAATG
66 CTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGATTGGACTAATG
42540 GC
131 GC
*
42542 TTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCATCACTACAG
1 TTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCATCACTACTG
* * * *
42607 GTTAGGGTGACAGAATCTGCAATCTACACCCTACTCCACCACTGCTTAGGGTGATTGGACTAATG
66 CTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGATTGGACTAATG
42672 GC
131 GC
*
42674 TTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCATCACTACAG
1 TTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCATCACTACTG
* * * *
42739 GTTAGGGTGACAGAATCTGCAATCTACACCCTACTCCACCACTGCTTAGGGTGATTGGACTAATG
66 CTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGATTGGACTAATG
42804 GC
131 GC
*
42806 TTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCATCACTACAG
1 TTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCATCACTACTG
* * *
42871 GTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATA
66 CTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGATTGGACTAATG
42936 GC
131 GC
* * * *
42938 TTAAATCTGCTTCTCCACTATATAGGGAAGATAAGATTCAGCATATTCGATCTGC-TCCACTACT
1 TTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCAT-CACTACT
* * *
43002 ACTTCGGGCGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGATTGGACTAAT
65 GCTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGATTGGACTAAT
43067 GGC
130 GGC
* *
43070 TTAAATCTGCTTCTCCACTGTATTGGGAA-AGTAAGATTCATCATATTCGATCTGC-TCCACTAC
1 TTAAATCTGCTTCTCCACTGTATTGGGAAGA-TAAGATTCACCATCTTCGATCTGCAT-CACTAC
* * * * * * * *
43133 TACTTCGGGCGACAGAATCTGCAATCTTCAACCAATTCCACTA-TAGCTTAGGGAGATAGGACAA
64 TGCTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACT-GCTTAGGGTGATTGGACTA
*
43197 ATGGA
128 ATGGC
* * * *
43202 TTAAATCTGCTTTTCCACTGTATTGGGAAAATAAGATTCACCACCTTCGATCTAC-TCCACTACT
1 TTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCAT-CACTACT
* * *
43266 GCTTAGGGTGACAAAATCTGCAATCTTCAACCTATTCGACTA---C-TA----GATTGGACTAAT
65 GCTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGATTGGACTAAT
43323 GGC
130 GGC
* * * * * * * *
43326 TGAAATCTGCTTCTCCAATATCTTGAGAAGATAAGAATCCCCATCTTCGATCCGC-TCCACTACT
1 TTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCAT-CACTACT
* * * * ** **
43390 GCTTAGGGGGACTGAATCTGCAATCTTTAACCTACTCCACTACTTCTTAGTCTGATAAGACTAAT
65 GCTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGATTGGACTAAT
*
43455 GGA
130 GGC
* * *
43458 TTAAATCTGCATCTCCACTATCTTGGGAAGATAAGATTCACCATCTTCGATCTGCATCACTACTG
1 TTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCATCACTACTG
* * * *
43523 ATTGGGGTGACAGAATCTGCAATCTACAACCTACTCCACTACTGCTTAGGGTGATTGGAGTAATG
66 CTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGATTGGACTAATG
43588 GC
131 GC
* * * * * * *
43590 TGAAATCTGCTTCTCCACTATCTTGAGAAGATAAGATTCATCATATTCGATCTGC-TCCGCTACT
1 TTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCAT-CACTACT
* * * * ** *
43654 GTTTAGGGTGACAGAATCTGAAATCTTCAACCTCCTCCAGTACTGCTTAACGTGAATGGACTAAT
65 GCTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGATTGGACTAAT
43719 GGC
130 GGC
43722 TTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCATCACTACTG
1 TTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCATCACTACTG
* * * * *
43787 ATTGGGGTGACAGAATCTGCAATCTACAACCTACTCTACTACTGCTTAGGGTGATTAGACTAATG
66 CTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGATTGGACTAATG
43852 GC
131 GC
43854 TTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCATCACTACTG
1 TTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCATCACTACTG
* * * * *
43919 ATTGGGGTGACAGAATCTGCAATCTACAACCTACTCTACTACTGCTTAGGGTGATTAGACTAATG
66 CTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGATTGGACTAATG
43984 GC
131 GC
43986 TTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCATCACTACTG
1 TTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCATCACTACTG
* * * * *
44051 ATTGGGGTGACAGAATCTGCAATCTACAACCTACTCTACTACTGCTTAGGGTGATTAGACTAATG
66 CTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGATTGGACTAATG
44116 GC
131 GC
44118 TTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCATCACTACTG
1 TTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCATCACTACTG
* * * *
44183 ATTGGGGTGACAGAATCTGCAATCTACAACCTACTCCACTACTGCTTAGGGTGATTGGAGTAATG
66 CTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGATTGGACTAATG
44248 GC
131 GC
* * * * * * *
44250 TGAAATCTGCTTCTCCACTATCTTGAGAAGATAAGATTCATCATATTCGATCTGC-TCCGCTACT
1 TTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCAT-CACTACT
*
44314 GTTTAGGGTGACAGAAT
65 GCTTAGGGTGACAGAAT
44331 TGCTTAGGGT
Statistics
Matches: 3248, Mismatches: 317, Indels: 114
0.88 0.09 0.03
Matches are distributed among these distances:
116 1 0.00
117 84 0.03
118 13 0.00
119 2 0.00
121 1 0.00
122 2 0.00
124 100 0.03
127 1 0.00
128 7 0.00
129 2 0.00
130 1 0.00
131 62 0.02
132 2939 0.90
133 33 0.01
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.31
Consensus pattern (132 bp):
TTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCATCACTACTG
CTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGATTGGACTAATG
GC
Found at i:41766 original size:117 final size:114
Alignment explanation
Indices: 41560--41789 Score: 363
Period size: 117 Copynumber: 2.0 Consensus size: 114
41550 ATCTGCTTCG
* *
41560 CTACTGTTTAGGGTGACAGAATCTGTAATCTTCAACCAATTCCACTATGGCTTAGGGAGATAGGA
1 CTACTGTTTAGGGTGACAGAATCTGTAATCTTCAACCAACTCCACTATCGCTTAGGGAGATAGGA
41625 CTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAAATAAGATTCAC
66 CTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAAATAAGATTCAC
* *
41674 NNNCTACTGTTTAGGGTGACAGAATCTGTAATCTTTCAACTAACTCCACTA-CGCTTAGGGTGAT
1 ---CTACTGTTTAGGGTGACAGAATCTGTAATC-TTCAACCAACTCCACTATCGCTTAGGGAGAT
* *
41738 TGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAAGTAAGATTCA
62 AGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAAATAAGATTCA
41790 TCATATTTCG
Statistics
Matches: 106, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
117 91 0.86
118 15 0.14
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.31
Consensus pattern (114 bp):
CTACTGTTTAGGGTGACAGAATCTGTAATCTTCAACCAACTCCACTATCGCTTAGGGAGATAGGA
CTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAAATAAGATTCAC
Found at i:44410 original size:106 final size:106
Alignment explanation
Indices: 44252--44535 Score: 428
Period size: 106 Copynumber: 2.7 Consensus size: 106
44242 GTAATGGCTG
* * * * *
44252 AAATCTGCTTCTCCACTATCTTGAGAAGATAAGATTCATCATATTCGATCTGCTCCGCTACTGTT
1 AAATCTGCTTCTCCACTGTATTGGGAAAATAAGATTCATCATATTCGATCTGCTCCACTACTGTT
44317 TAGGGTGACAGAATTGCTTAGGGTGTTAAAACTAATCGATT
66 TAGGGTGACAGAATTGCTTAGGGTGTTAAAACTAATCGATT
*
44358 AAATCTGCTTCTCCACTGTATTGGGAAAATAAGATTCATCATATTCGATCTGCTTCACTACTGTT
1 AAATCTGCTTCTCCACTGTATTGGGAAAATAAGATTCATCATATTCGATCTGCTCCACTACTGTT
*
44423 TAGGGTGACTGAATTGCTTAGGGTGTTAAAACTAATCGATT
66 TAGGGTGACAGAATTGCTTAGGGTGTTAAAACTAATCGATT
* * * *
44464 AATTCTGCTTCTCCACTGTATTGGGAAATTAAGATTC-GC-TATCATCGATCTACTCCACTACTG
1 AAATCTGCTTCTCCACTGTATTGGGAAAATAAGATTCATCATAT--TCGATCTGCTCCACTACTG
*
44527 CTTAGGGTG
64 TTTAGGGTG
44536 CTTGGAGTAA
Statistics
Matches: 163, Mismatches: 13, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
104 3 0.02
105 1 0.01
106 159 0.98
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.35
Consensus pattern (106 bp):
AAATCTGCTTCTCCACTGTATTGGGAAAATAAGATTCATCATATTCGATCTGCTCCACTACTGTT
TAGGGTGACAGAATTGCTTAGGGTGTTAAAACTAATCGATT
Found at i:44586 original size:88 final size:88
Alignment explanation
Indices: 44467--44933 Score: 907
Period size: 88 Copynumber: 5.3 Consensus size: 88
44457 ATCGATTAAT
44467 TCTGCTTCTCCACTGTATTGGGAAATTAAGATTCGCTATCATCGATCTACTCCACTACTGCTTAG
1 TCTGCTTCTCCACTGTATTGGGAAATTAAGATTCGCTATCATCGATCTACTCCACTACTGCTTAG
44532 GGTGCTTGGAGTAATGGCTGAAA
66 GGTGCTTGGAGTAATGGCTGAAA
44555 TCTGCTTCTCCACTGTATTGGGAAATTAAGATTCGCTATCATCGATCTACTCCACTACTGCTTAG
1 TCTGCTTCTCCACTGTATTGGGAAATTAAGATTCGCTATCATCGATCTACTCCACTACTGCTTAG
44620 GGTGCTTGGAGTAATGGCTGAAA
66 GGTGCTTGGAGTAATGGCTGAAA
44643 TCTGCTTCTCCACTGTATTGGGAAATTAAGATTCGCTATCATCGATCTACTCCACTACTGCTTAG
1 TCTGCTTCTCCACTGTATTGGGAAATTAAGATTCGCTATCATCGATCTACTCCACTACTGCTTAG
44708 GGTGCTTGGAGTAATGGCTGAAA
66 GGTGCTTGGAGTAATGGCTGAAA
44731 TCTGCTTCTCCACTGTATTGGGAAATTAAGATTCGCTATCATCGATCTACTCCACTACTGCTTAG
1 TCTGCTTCTCCACTGTATTGGGAAATTAAGATTCGCTATCATCGATCTACTCCACTACTGCTTAG
44796 GGTGCTTGGAGTAATGGCTGAAA
66 GGTGCTTGGAGTAATGGCTGAAA
44819 TCTGCTTCTCCACTGTATTGGGAAATTAAGATTCGCTATCATCGATCTACTCCACTACTGCTTAG
1 TCTGCTTCTCCACTGTATTGGGAAATTAAGATTCGCTATCATCGATCTACTCCACTACTGCTTAG
* * *
44884 GGTGATTGGACTAATGGCTTAAA
66 GGTGCTTGGAGTAATGGCTGAAA
44907 TCTGCTTCTCCACTGTATTGGGAAATT
1 TCTGCTTCTCCACTGTATTGGGAAATT
44934 GATAATTATC
Statistics
Matches: 376, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
88 376 1.00
ACGTcount: A:0.24, C:0.22, G:0.21, T:0.34
Consensus pattern (88 bp):
TCTGCTTCTCCACTGTATTGGGAAATTAAGATTCGCTATCATCGATCTACTCCACTACTGCTTAG
GGTGCTTGGAGTAATGGCTGAAA
Found at i:45102 original size:132 final size:132
Alignment explanation
Indices: 44865--45654 Score: 1056
Period size: 132 Copynumber: 6.0 Consensus size: 132
44855 TATCATCGAT
* *
44865 CTACTCCACTACTGCTTAGGGTGATTGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGA
1 CTACTCCACTACTACTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGA
* * *
44930 AATTGATA-ATT-ATCATATTCGATCTGCTTCACTACTGTTTAGGGTGACAGAATCTGCAATCTT
66 AAAT-A-AGATTCATCATATTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTT
44993 CAAC
129 CAAC
44997 CTACTCCACTACTACTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGA
1 CTACTCCACTACTACTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGA
* * *
45062 AATTGATA-ATT-ATCATATTCGATCTGCTTCACTACTGTTTAGGGTGACAGAATCTGCAATCTT
66 AAAT-A-AGATTCATCATATTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTT
45125 CAAC
129 CAAC
* *
45129 CTACTCCACTACTACTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACCGTATTTGGA
1 CTACTCCACTACTACTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGA
** * * * * * *
45194 AGGTAAGATTCAGCATCTTCGATCTACTCCACTACTGCTTAGTGTGACAGAATTTGTAATCTTCA
66 AAATAAGATTCATCATATTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTCA
45259 AC
131 AC
* * * *
45261 CTACTCAACTGCTACTTAGGGTGATTGGACTAATGGCTTAAATTTGCTTCTCCACTGTATTGGGA
1 CTACTCCACTACTACTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGA
* * *
45326 AAATAAGATTCATCATATTCGATCTGCTTCACTACTGTTTAGGGTGACAGAATCTGTAATCTTCA
66 AAATAAGATTCATCATATTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTCA
45391 AC
131 AC
* * * * *
45393 CAATTCCACTA-TGGCTTAGGGAGATAGGGCTAATGGCTTAAATCTGCTTCTCCACTGTATTGGG
1 CTACTCCACTACT-ACTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGG
* * * *
45457 AAAATAAGATTCACCATCTTCGATCTACTCCAATACTGCTTAGGGTGACAGAATCTGCAATCTTC
65 AAAATAAGATTCATCATATTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTC
45522 AAC
130 AAC
* * * * * * *
45525 CTACTCCTCTACTGCTTAGGGAGATTA-GACTAATGGC-TCAATCTGCTTCTCCACTATCTTGAG
1 CTACTCCACTACTACTTAGGGTGA-TAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGG
* * * *
45588 AAGATAAGAATCA-CTATCTTCGATCTGCTCCACTACTGCTTAGGGTTACAGAATCTGCAATCTT
65 AAAATAAGATTCATC-ATATTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTT
45652 CAA
129 CAA
Statistics
Matches: 594, Mismatches: 58, Indels: 13
0.89 0.09 0.02
Matches are distributed among these distances:
130 2 0.00
131 87 0.15
132 502 0.85
133 3 0.01
ACGTcount: A:0.27, C:0.22, G:0.18, T:0.33
Consensus pattern (132 bp):
CTACTCCACTACTACTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGA
AAATAAGATTCATCATATTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTCA
AC
Done.